RCSB PDB

Look up and search the Protein Data Bank's 3D structures of proteins, DNA and RNA: get a structure, its molecules, chains, assemblies and ligands, chemical components, UniProt details and papers; find structures by text, organism, method, resolution, release date, sequence, chemistry or shape; check status; and get file links.

Actions

Action	What it does
Check structure status	Check up to 100 PDB IDs at once: whether each is released, waiting for release or removed, and what replaced a removed one.
Find ligands by chemical structure	Find ligands in the PDB's chemical dictionary from a molecule you describe as SMILES, InChI or a formula: the same molecule, similar ones, or ones that contain it.
Find similar sequences	Find molecules in the PDB whose protein, DNA or RNA sequence is like yours, best match first, with how identical each is and its E-value.
Find structures by organism, method and date	Find structures that match every filter you set: organism, how they were solved, what they contain, how sharp they are, when they were released, a ligand they bind, and keywords.
Find structures with a similar shape	Find structures whose overall 3D shape is like one structure's assembly, whatever their sequence, best match first.
Get a biological assembly	Get the form a structure's molecules are thought to take in the cell: how many chains, its symmetry and stoichiometry (such as A2B2), and who defined it.
Get a chain	Get one chain of a structure: which molecule it is, how many residues were modelled, how much is helix and strand, its CATH, SCOP and ECOD domains, and the ligands touching it.
Get a chemical component	Look up a ligand in the PDB's chemical dictionary by its ID, such as HEM or ATP: its name, formula, weight, SMILES and InChIKey, its IDs in DrugBank, PubChem, ChEBI and ChEMBL, and the proteins it is known to act on.
Get a ligand in a structure	Get one small molecule bound in a structure, such as a heme or a drug: its ligand ID and name, how many copies there are, and which chains they sit on.
Get a molecule from a structure	Get one protein, DNA or RNA in a structure: its name, sequence and length, its chains, the organism and genes it comes from, and its UniProt IDs and Pfam families.
Get a removed structure	Get what the PDB still records about a structure it removed: its title, authors, dates, why it was removed and which structures replaced it.
Get a structure	Get a structure's title, how it was solved and at what resolution, its dates, authors and paper, and the numbers of the molecules, ligands and assemblies in it.
Get a structure's file links	Get download links for a structure's files: the model as mmCIF, PDB format and BinaryCIF, its sequences as FASTA, each assembly, and the X-ray data or EM maps when they were released.
Get a structure's paper	Get the paper that describes a structure: title, journal, authors, abstract and subject headings, with links by DOI and on PubMed.
Get an unreleased structure	Get a structure that has been deposited but not released: its title, when it was deposited, and why it is waiting, such as being held until its paper is published.
Get several structures	Get up to 100 structures in one step, each with its title, method, resolution, release date, organisms and paper.
Get UniProt details for a molecule	Get the UniProt protein a molecule in a structure matches: its accession, name, function, genes, organism, full sequence, keywords and Gene Ontology terms.
Search structures	Search every structure's titles, descriptions, keywords, authors and papers for words, such as a protein, a disease or a gene, and get each match's title, method, resolution and organisms.

Check structure status

Check up to 100 PDB IDs at once: whether each is released, waiting for release or removed, and what replaced a removed one. IDs the PDB has never had are listed separately.

Inputs

PDB IDspdb_idslistRequired: Up to 100 structure IDs: a list from an earlier step, or IDs separated by commas, spaces or new lines, such as 4HHB, 1CRN.

Outputs

currentnumber: How many are released
entrieslist: Each ID the PDB knows, in the order asked
removednumber: How many were removed
unknownlist: IDs the PDB has never had
unreleasednumber: How many are waiting for release

Example output

{
  "current": 1,
  "entries": [
    {
      "pdb_id": "4HHB",
      "replaced_by": null,
      "status": "current",
      "status_code": "REL",
      "status_detail": null,
      "url": "https://www.rcsb.org/structure/4HHB"
    },
    {
      "pdb_id": "1JYY",
      "replaced_by": "4V44",
      "status": "removed",
      "status_code": "OBS",
      "status_detail": null,
      "url": null
    },
    {
      "pdb_id": "1ZSM",
      "replaced_by": null,
      "status": "unreleased",
      "status_code": "WDRN",
      "status_detail": "Withdrawn by the authors",
      "url": null
    }
  ],
  "removed": 1,
  "unknown": [
    "0ZZZ"
  ],
  "unreleased": 1
}

Find ligands by chemical structure

Find ligands in the PDB's chemical dictionary from a molecule you describe as SMILES, InChI or a formula: the same molecule, similar ones, or ones that contain it. Use the ligand IDs found with Find structures by organism, method and date to get the structures they are bound in.

Inputs

Describe it asinput_typetext: How the molecule is written in **Molecule**.One of: smiles, inchi, formula (Chemical formula). Default: smiles.
MoleculevaluetextRequired: The molecule as SMILES (aspirin is CC(=O)Oc1ccccc1C(=O)O), as InChI, or as a formula such as C9H8O4.
Matchmatchtext: Which molecules count as a match.Only when Describe it as is SMILES or InChI. One of: graph-strict (Exactly this molecule), graph-relaxed (This molecule, ignoring stereochemistry and charges), fingerprint-similarity (Similar molecules), sub-struct-graph-relaxed (Molecules that contain this one). Default: graph-relaxed.
Allow larger formulasformula_is_parttrue/false: Also find molecules whose formula contains this one, such as C9H8O4 within C10H10O4.Only when Describe it as is Chemical formula. Default: false.
Max resultsmax_resultsnumber: Return at most this many results.From 1 to 100. Default: 10.
Skipskipnumber: Leave out this many results from the start, to get the next page. With Max results at 10, a Skip of 10 gives results 11 to 20.From 0 to 10000. Default: 0.

Outputs

countnumber: How many came back in this step
has_moretrue/false: Whether more results are left after these (raise Skip to get them)
matchtext: How molecules were matched
resultslist: Ligands found, best first
totalnumber: How many match in all, across every page

Example output

{
  "count": 2,
  "has_more": true,
  "match": "fingerprint-similarity",
  "results": [
    {
      "formula": "C9 H8 O4",
      "image_url": "https://cdn.rcsb.org/images/ccd/labeled/A/AIN.svg",
      "inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
      "ligand_id": "AIN",
      "molecular_weight_da": 180.157,
      "name": "2-(ACETYLOXY)BENZOIC ACID",
      "score": 1.0,
      "smiles": "CC(=O)Oc1ccccc1C(=O)O",
      "url": "https://www.rcsb.org/ligand/AIN"
    },
    {
      "formula": "C10 H10 O4",
      "image_url": "https://cdn.rcsb.org/images/ccd/labeled/M/M3S.svg",
      "inchikey": "XRBMKGUDDJPAMH-UHFFFAOYSA-N",
      "ligand_id": "M3S",
      "molecular_weight_da": 194.184,
      "name": "2-(acetyloxy)-3-methylbenzoic acid",
      "score": 0.9444,
      "smiles": "Cc1cccc(c1OC(=O)C)C(=O)O",
      "url": "https://www.rcsb.org/ligand/M3S"
    }
  ],
  "total": 6
}

Find similar sequences

Find molecules in the PDB whose protein, DNA or RNA sequence is like yours, best match first, with how identical each is and its E-value. Paste a plain sequence or FASTA.

Inputs

SequencesequencetextRequired: The sequence in one-letter codes, at least 10 long, such as MVLSPADKTNVKAAWG... A FASTA header line is ignored.
Sequence typesequence_typetext: Whether the sequence is a protein, DNA or RNA.One of: protein, dna, rna. Default: protein.
Max E-valuemax_evaluenumber: Leave out matches likelier than this to be chance. Smaller is stricter; 0.1 is the PDB's default.From 0 to 1000. Default: 0.1.
Min identity (%)min_identitynumber: Leave out matches with fewer identical residues than this, in percent. 0 keeps every match; 90 keeps near copies.From 0 to 100. Default: 0.
Max resultsmax_resultsnumber: Return at most this many results.From 1 to 100. Default: 10.
Skipskipnumber: Leave out this many results from the start, to get the next page. With Max results at 10, a Skip of 10 gives results 11 to 20.From 0 to 10000. Default: 0.

Outputs

countnumber: How many came back in this step
has_moretrue/false: Whether more results are left after these (raise Skip to get them)
resultslist: Molecules with a similar sequence, best first
sequence_lengthnumber: Length of the sequence searched with
totalnumber: How many match in all, across every page

Example output

{
  "count": 2,
  "has_more": true,
  "results": [
    {
      "aligned_length": 141,
      "chains": [
        "A",
        "C"
      ],
      "description": "HEMOGLOBIN (ALPHA CHAIN)",
      "evalue": 2.821e-89,
      "experimental_method": "X-ray",
      "identity_percent": 100.0,
      "key": "1A00_1",
      "length": 141,
      "match_end": 141,
      "match_start": 1,
      "molecule_id": "1",
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "1A00",
      "query_end": 141,
      "query_start": 1,
      "resolution_angstrom": 2.0,
      "structure_title": "HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 TYR) MUTANT",
      "url": "https://www.rcsb.org/structure/1A00"
    },
    {
      "aligned_length": 141,
      "chains": [
        "A",
        "C"
      ],
      "description": "HEMOGLOBIN (ALPHA CHAIN)",
      "evalue": 2.821e-89,
      "experimental_method": "X-ray",
      "identity_percent": 100.0,
      "key": "1A01_1",
      "length": 141,
      "match_end": 141,
      "match_start": 1,
      "molecule_id": "1",
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "1A01",
      "query_end": 141,
      "query_start": 1,
      "resolution_angstrom": 1.8,
      "structure_title": "HEMOGLOBIN (VAL BETA1 MET, TRP BETA37 ALA) MUTANT",
      "url": "https://www.rcsb.org/structure/1A01"
    }
  ],
  "sequence_length": 141,
  "total": 359
}

Find structures by organism, method and date

Find structures that match every filter you set: organism, how they were solved, what they contain, how sharp they are, when they were released, a ligand they bind, and keywords. Set at least one.

Inputs

Organismorganismtext: The organism the molecules come from, by its scientific name, such as Homo sapiens or Escherichia coli.
Methodsmethodslist: How the structure was solved. Choose none to allow any.One or more of: X-ray (X-ray crystallography), EM (Cryo-electron microscopy (EM)), NMR, Neutron (Neutron diffraction), Multiple methods (More than one method), Other (Other methods).
Molecule typesmolecule_typeslist: What the structure is made of. Choose none to allow any.One or more of: Protein (only) (Protein only), Protein/NA (Protein with DNA or RNA), Nucleic acid (only) (DNA or RNA only), Protein/Oligosaccharide (Protein with sugars), Oligosaccharide (only) (Sugars only), Other.
Resolution at least (Å)max_resolutionnumber: Only structures this sharp or sharper, in ångströms. Smaller numbers are sharper; 2 is a good X-ray structure. Leaves out NMR, which has no resolution.From 0.1 to 100.
Released on or afterreleased_afterdate: Only structures first released on or after this day.
Released on or beforereleased_beforedate: Only structures first released on or before this day.
Contains ligandligand_idtext: Only structures with this ligand bound, by its ID, such as HEM for heme or ATP.
Keywordskeywordstext: Only structures whose text mentions these words.
Sort bysorttext: The order to list structures in.One of: relevance (Best match first), newest (Newest first), oldest (Oldest first), resolution (Sharpest resolution first). Default: newest.
Max resultsmax_resultsnumber: Return at most this many results.From 1 to 100. Default: 10.
Skipskipnumber: Leave out this many results from the start, to get the next page. With Max results at 10, a Skip of 10 gives results 11 to 20.From 0 to 10000. Default: 0.

Outputs

countnumber: How many came back in this step
filtersobject: The filters the search used
has_moretrue/false: Whether more results are left after these (raise Skip to get them)
resultslist: The structures found
totalnumber: How many match in all, across every page

Example output

{
  "count": 2,
  "filters": {
    "keywords": null,
    "ligand_id": null,
    "max_resolution": 1.5,
    "methods": [
      "X-ray"
    ],
    "molecule_types": [],
    "organism": "Homo sapiens",
    "released_after": "2024-01-01",
    "released_before": "2024-01-31"
  },
  "has_more": true,
  "results": [
    {
      "doi": "10.1039/d4sc00367e",
      "experimental_method": "X-ray",
      "keywords": "HYDROLASE",
      "molecular_weight_kda": 39.37,
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "8C8B",
      "pubmed_id": 38817593,
      "release_date": "2024-01-31",
      "resolution_angstrom": 1.46,
      "score": 1.0,
      "title": "Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48).",
      "url": "https://www.rcsb.org/structure/8C8B"
    },
    {
      "doi": "10.1039/d4sc00367e",
      "experimental_method": "X-ray",
      "keywords": "HYDROLASE",
      "molecular_weight_kda": 39.77,
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "8C8D",
      "pubmed_id": 38817593,
      "release_date": "2024-01-31",
      "resolution_angstrom": 1.46,
      "score": 1.0,
      "title": "Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 44).",
      "url": "https://www.rcsb.org/structure/8C8D"
    }
  ],
  "total": 24
}

Find structures with a similar shape

Find structures whose overall 3D shape is like one structure's assembly, whatever their sequence, best match first.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
Assemblyassemblytext: The biological assembly: the form the molecules are thought to take in the cell, such as a dimer. Most structures have only assembly 1.Default: 1.
How similarmatchtext: Closely similar finds near copies; broadly similar also finds looser resemblances.One of: strict_shape_match (Closely similar shape), relaxed_shape_match (Broadly similar shape). Default: strict_shape_match.
Max resultsmax_resultsnumber: Return at most this many results.From 1 to 100. Default: 10.
Skipskipnumber: Leave out this many results from the start, to get the next page. With Max results at 10, a Skip of 10 gives results 11 to 20.From 0 to 10000. Default: 0.

Outputs

assembly_idtext: The assembly whose shape was compared
countnumber: How many came back in this step
has_moretrue/false: Whether more results are left after these (raise Skip to get them)
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
resultslist: The structures found
totalnumber: How many match in all, across every page

Example output

{
  "assembly_id": "1",
  "count": 2,
  "has_more": true,
  "pdb_id": "4HHB",
  "results": [
    {
      "doi": "10.1016/0022-2836(84)90472-8",
      "experimental_method": "X-ray",
      "keywords": "OXYGEN TRANSPORT",
      "molecular_weight_kda": 64.74,
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "4HHB",
      "pubmed_id": 6726807,
      "release_date": "1984-07-17",
      "resolution_angstrom": 1.74,
      "score": 1.0,
      "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION",
      "url": "https://www.rcsb.org/structure/4HHB"
    },
    {
      "doi": "10.1016/0022-2836(89)90579-2",
      "experimental_method": "X-ray",
      "keywords": "OXYGEN TRANSPORT",
      "molecular_weight_kda": 64.61,
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "1COH",
      "pubmed_id": 2738915,
      "release_date": "1990-01-15",
      "resolution_angstrom": 2.9,
      "score": 0.9892,
      "title": "STRUCTURE OF HAEMOGLOBIN IN THE DEOXY QUATERNARY STATE WITH LIGAND BOUND AT THE ALPHA HAEMS",
      "url": "https://www.rcsb.org/structure/1COH"
    }
  ],
  "total": 1406
}

Get a biological assembly

Get the form a structure's molecules are thought to take in the cell: how many chains, its symmetry and stoichiometry (such as A2B2), and who defined it.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
Assemblyassemblytext: The biological assembly: the form the molecules are thought to take in the cell, such as a dimer. Most structures have only assembly 1.Default: 1.

Outputs

assembly_idtext: The assembly's number
atom_countnumber: Atoms in the assembly
buried_surface_areanumber: Surface buried between chains, in square ångströms
chain_countnumber: Chains in the assembly
determined_bytext: Who defined it: the authors, software, or both
interface_countnumber: Contacts between chains
ligand_countnumber: Ligand copies in the assembly
molecular_weight_kdanumber: Total molecular weight, in kilodaltons
oligomeric_statetext: What it is, such as Hetero 4-mer or Monomer
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
softwaretext: The program that suggested it, such as PISA
stoichiometrytext: How many of each molecule, such as A2B2
symmetrytext: Its symmetry, such as C2; C1 means none
symmetry_typetext: Kind of symmetry, such as Cyclic or Dihedral
urltext: The structure's page on rcsb.org

Example output

{
  "assembly_id": "1",
  "atom_count": 4779,
  "buried_surface_area": 3305.3493,
  "chain_count": 4,
  "determined_by": "author and software defined assembly",
  "interface_count": 5,
  "ligand_count": 6,
  "molecular_weight_kda": 64.74,
  "oligomeric_state": "Hetero 4-mer",
  "pdb_id": "4HHB",
  "software": "PISA",
  "stoichiometry": "A2B2",
  "symmetry": "C2",
  "symmetry_type": "Cyclic",
  "url": "https://www.rcsb.org/structure/4HHB"
}

Get a chain

Get one chain of a structure: which molecule it is, how many residues were modelled, how much is helix and strand, its CATH, SCOP and ECOD domains, and the ligands touching it.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
ChainchaintextRequired: One copy of a molecule, such as chain A. The letter a paper uses works, and so does the PDB's own chain ID. Fill in **PDB ID** first to pick from its chains.

Outputs

chain_idtext: The authors' chain letter, as papers and viewers show it
domainslist: Structural domains assigned to the chain
helix_percentnumber: Share of the chain in helices, in percent
ligands_nearbylist: IDs of ligands that touch the chain
modeled_residue_countnumber: Residues with coordinates in the model
molecule_idtext: The number of the molecule this chain is a copy of
molecule_keytext: The structure and molecule together, such as 4HHB_1
pdb_chain_idtext: The PDB's own chain ID, which can differ
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
strand_percentnumber: Share of the chain in beta strands, in percent
urltext: The structure's page on rcsb.org

Example output

{
  "chain_id": "A",
  "domains": [
    {
      "id": "1.10.490.10",
      "name": "Globins",
      "source": "CATH"
    },
    {
      "id": "d4hhba_",
      "name": "Hemoglobin, alpha-chain",
      "source": "SCOP"
    },
    {
      "id": "8039836",
      "name": "Globin-like",
      "source": "SCOP2"
    },
    {
      "id": "e4hhbA1",
      "name": "Bcl-2",
      "source": "ECOD"
    }
  ],
  "helix_percent": 78.0,
  "ligands_nearby": [
    "HEM"
  ],
  "modeled_residue_count": 141,
  "molecule_id": "1",
  "molecule_key": "4HHB_1",
  "pdb_chain_id": "A",
  "pdb_id": "4HHB",
  "strand_percent": 0.0,
  "url": "https://www.rcsb.org/structure/4HHB"
}

Get a chemical component

Look up a ligand in the PDB's chemical dictionary by its ID, such as HEM or ATP: its name, formula, weight, SMILES and InChIKey, its IDs in DrugBank, PubChem, ChEBI and ChEMBL, and the proteins it is known to act on.

Inputs

Ligand IDligand_idtextRequired: The ligand's ID in the PDB's chemical dictionary, up to five letters or digits, such as HEM for heme, ATP, or AIN for aspirin.

Outputs

atom_countnumber: Atoms, hydrogens included
drug_targetslist: Proteins DrugBank lists it acting on
external_idsobject: Its IDs in other chemistry databases
first_releasedtext: When it first appeared in the PDB (YYYY-MM-DD)
formulatext: Its formula, such as C34 H32 Fe N4 O4
heavy_atom_countnumber: Atoms other than hydrogen
image_urltext: A 2D drawing of it (SVG)
inchitext: Its InChI
inchikeytext: Its InChIKey, for matching across databases
ligand_idtext: The ligand's ID, such as HEM
molecular_weight_danumber: Molecular weight, in daltons
nametext: Its chemical name
sdf_urltext: Its ideal 3D coordinates as an SDF file
smilestext: Its structure as SMILES, with stereochemistry
synonymslist: Other names for it
typetext: Kind of component, such as non-polymer or L-peptide linking
urltext: The ligand's page on rcsb.org

Example output

{
  "atom_count": 75,
  "drug_targets": [
    {
      "actions": [
        "inhibitor"
      ],
      "name": "Nitric oxide synthase, inducible",
      "uniprot_id": "P35228"
    },
    {
      "actions": [
        "inhibitor"
      ],
      "name": "Cytochrome P450 3A4",
      "uniprot_id": "P08684"
    },
    {
      "actions": [
        "inhibitor"
      ],
      "name": "Nitric oxide synthase 1",
      "uniprot_id": "P29475"
    },
    {
      "actions": [
        "inhibitor"
      ],
      "name": "Hemoglobin subunit alpha",
      "uniprot_id": "P69905"
    }
  ],
  "external_ids": {
    "cas": null,
    "chebi": null,
    "chembl": null,
    "drugbank": "DB18267",
    "pubchem": null
  },
  "first_released": "1976-05-19",
  "formula": "C34 H32 Fe N4 O4",
  "heavy_atom_count": 43,
  "image_url": "https://cdn.rcsb.org/images/ccd/labeled/H/HEM.svg",
  "inchi": "InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;",
  "inchikey": "KABFMIBPWCXCRK-RGGAHWMASA-L",
  "ligand_id": "HEM",
  "molecular_weight_da": 616.487,
  "name": "PROTOPORPHYRIN IX CONTAINING FE",
  "sdf_url": "https://files.rcsb.org/ligands/download/HEM_ideal.sdf",
  "smiles": "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O",
  "synonyms": [
    "PROTOPORPHYRIN IX CONTAINING FE",
    "HEME",
    "3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid",
    "[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]iron"
  ],
  "type": "non-polymer",
  "url": "https://www.rcsb.org/ligand/HEM"
}

Get a ligand in a structure

Get one small molecule bound in a structure, such as a heme or a drug: its ligand ID and name, how many copies there are, and which chains they sit on.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
Ligandligand_entity_idtextRequired: Which small molecule bound in the structure, such as a heme or a drug. Fill in **PDB ID** first to pick from its ligands.

Outputs

chainslist: Chains it is bound to
copiesnumber: How many copies are bound
ligand_entity_idtext: The ligand's number in the structure
ligand_idtext: Its chemical component ID, such as HEM
ligand_urltext: The ligand's page on rcsb.org
molecular_weight_danumber: Molecular weight, in daltons
nametext: Its chemical name
pdb_idtext: The structure's four-character PDB ID, such as 4HHB

Example output

{
  "chains": [
    "A",
    "B",
    "C",
    "D"
  ],
  "copies": 4,
  "ligand_entity_id": "3",
  "ligand_id": "HEM",
  "ligand_url": "https://www.rcsb.org/ligand/HEM",
  "molecular_weight_da": 616.0,
  "name": "PROTOPORPHYRIN IX CONTAINING FE",
  "pdb_id": "4HHB"
}

Get a molecule from a structure

Get one protein, DNA or RNA in a structure: its name, sequence and length, its chains, the organism and genes it comes from, and its UniProt IDs and Pfam families.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
Moleculemolecule_idtextRequired: Which molecule in the structure: each different protein, DNA or RNA has a number, starting at 1, shared by all its copies. Fill in **PDB ID** first to pick from its molecules.

Outputs

chainslist: The authors' chain letters for its copies
copiesnumber: How many copies are in the structure
descriptiontext: What the molecule is, such as Hemoglobin subunit alpha
expressed_inlist: Organisms it was made in for the experiment, if recorded
geneslist: Gene names it comes from, such as HBA1
keytext: The structure and molecule together, such as 4HHB_1
lengthnumber: Number of residues
molecular_weight_kdanumber: Molecular weight of one copy, in kilodaltons
molecule_idtext: The molecule's number in the structure
mutation_countnumber: Mutations compared with the natural sequence
organismslist: Scientific names of the organisms the molecules come from
pdb_chain_idslist: The PDB's own chain IDs for its copies
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
pfam_domainslist: Pfam protein families found in it
sequencetext: Its sequence in one-letter codes
taxonomy_idslist: NCBI taxonomy IDs of those organisms
typetext: Protein, DNA, RNA or another polymer type
uniprot_idslist: Matching UniProt accessions, such as P69905
urltext: The structure's page on rcsb.org

Example output

{
  "chains": [
    "A",
    "C"
  ],
  "copies": 2,
  "description": "Hemoglobin subunit alpha",
  "expressed_in": [],
  "genes": [
    "HBA1",
    "HBA2"
  ],
  "key": "4HHB_1",
  "length": 141,
  "molecular_weight_kda": 15.15,
  "molecule_id": "1",
  "mutation_count": 0,
  "organisms": [
    "Homo sapiens"
  ],
  "pdb_chain_ids": [
    "A",
    "C"
  ],
  "pdb_id": "4HHB",
  "pfam_domains": [
    {
      "id": "PF00042",
      "name": "Globin (Globin)"
    }
  ],
  "sequence": "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
  "taxonomy_ids": [
    9606
  ],
  "type": "Protein",
  "uniprot_ids": [
    "P69905"
  ],
  "url": "https://www.rcsb.org/structure/4HHB"
}

Get a removed structure

Get what the PDB still records about a structure it removed: its title, authors, dates, why it was removed and which structures replaced it.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.

Outputs

authorslist: Who deposited it
deposit_datetext: When it was deposited (YYYY-MM-DD)
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
reasontext: Why it was removed, when the PDB says
release_datetext: When it was released (YYYY-MM-DD)
removed_datetext: When it was removed (YYYY-MM-DD)
replaced_bylist: IDs that replaced it
replacement_urltext: The page of the first replacement
titletext: The title the authors gave the structure

Example output

{
  "authors": [
    "Juers, D.H.",
    "McCarter, J.D.",
    "Withers, S.G.",
    "Matthews, B.W."
  ],
  "deposit_date": "2001-09-13",
  "pdb_id": "1JYY",
  "reason": "This entry with other split entries have been consolidated into a combined file for complete representation. No coordinates have been changed.",
  "release_date": "2001-12-07",
  "removed_date": "2014-12-10",
  "replaced_by": [
    "4V44"
  ],
  "replacement_url": "https://www.rcsb.org/structure/4V44",
  "title": "E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE. Chains A-H, see REMARK 400."
}

Get a structure

Get a structure's title, how it was solved and at what resolution, its dates, authors and paper, and the numbers of the molecules, ligands and assemblies in it.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.

Outputs

assembly_idslist: Numbers of its biological assemblies, for Get a biological assembly
atom_countnumber: Atoms in the deposited model
authorslist: Who deposited it
chain_countnumber: Chains (protein, DNA or RNA) in the deposited model
citationobject: The paper that describes it, if any
compositiontext: What it is made of, such as 'heteromeric protein'
deposit_datetext: When it was deposited (YYYY-MM-DD)
doitext: The structure's own DOI, for citing the data
emdb_idslist: Electron microscopy maps behind it, such as EMD-5639
experimental_methodtext: How the structure was solved: X-ray, EM, NMR, Neutron, Multiple methods or Other
is_computed_modeltrue/false: True for a computed model (such as AlphaFold), false for an experiment
keywordstext: The PDB's classification, such as OXYGEN TRANSPORT
ligand_entity_idslist: Numbers of its ligands, for Get a ligand in a structure
ligand_idslist: IDs of the ligands bound to it, such as HEM, for Get a chemical component
methodslist: Each method in full, such as X-RAY DIFFRACTION
molecular_weight_kdanumber: Total molecular weight, in kilodaltons
molecule_idslist: Numbers of its molecules (proteins, DNA, RNA), for Get a molecule
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
release_datetext: When it was first released (YYYY-MM-DD)
replaceslist: Older PDB IDs this structure replaced
resolution_angstromnumber: Resolution in ångströms (Å); smaller means finer detail. Empty for NMR and computed models
revision_datetext: When it was last revised (YYYY-MM-DD)
titletext: The title the authors gave the structure
urltext: The structure's page on rcsb.org

Example output

{
  "assembly_ids": [
    "1"
  ],
  "atom_count": 4779,
  "authors": [
    "Fermi, G.",
    "Perutz, M.F."
  ],
  "chain_count": 4,
  "citation": {
    "authors": [
      "Fermi, G.",
      "Perutz, M.F.",
      "Shaanan, B.",
      "Fourme, R."
    ],
    "doi": "10.1016/0022-2836(84)90472-8",
    "journal": "J Mol Biol",
    "pages": "159-174",
    "pubmed_id": 6726807,
    "title": "The crystal structure of human deoxyhaemoglobin at 1.74 A resolution",
    "volume": "175",
    "year": 1984
  },
  "composition": "heteromeric protein",
  "deposit_date": "1984-03-07",
  "doi": "10.2210/pdb4hhb/pdb",
  "emdb_ids": [],
  "experimental_method": "X-ray",
  "is_computed_model": false,
  "keywords": "OXYGEN TRANSPORT",
  "ligand_entity_ids": [
    "3",
    "4"
  ],
  "ligand_ids": [
    "HEM"
  ],
  "methods": [
    "X-RAY DIFFRACTION"
  ],
  "molecular_weight_kda": 64.74,
  "molecule_ids": [
    "1",
    "2"
  ],
  "pdb_id": "4HHB",
  "release_date": "1984-07-17",
  "replaces": [
    "1HHB"
  ],
  "resolution_angstrom": 1.74,
  "revision_date": "2026-08-12",
  "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION",
  "url": "https://www.rcsb.org/structure/4HHB"
}

Get a structure's file links

Get download links for a structure's files: the model as mmCIF, PDB format and BinaryCIF, its sequences as FASTA, each assembly, and the X-ray data or EM maps when they were released. Formats a structure is not published in are left empty.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.

Outputs

assemblieslist: Files for each biological assembly
bcif_urltext: The model as BinaryCIF, a compact format for viewers
em_mapslist: Electron microscopy maps
fasta_urltext: The sequences of every molecule, as FASTA
has_pdb_formattrue/false: Whether a legacy PDB-format file exists
mmcif_gz_urltext: The same mmCIF file, compressed
mmcif_urltext: The model as mmCIF, the standard format
page_urltext: The structure's page on rcsb.org
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
pdb_urltext: The model in the legacy PDB format; empty for structures too large for it
structure_factors_urltext: The X-ray data (structure factors), when the authors released it

Example output

{
  "assemblies": [
    {
      "assembly_id": "1",
      "image_url": "https://cdn.rcsb.org/images/structures/4hhb_assembly-1.jpeg",
      "mmcif_url": "https://files.rcsb.org/download/4HHB-assembly1.cif.gz"
    }
  ],
  "bcif_url": "https://models.rcsb.org/4HHB.bcif",
  "em_maps": [],
  "fasta_url": "https://www.rcsb.org/fasta/entry/4HHB",
  "has_pdb_format": true,
  "mmcif_gz_url": "https://files.rcsb.org/download/4HHB.cif.gz",
  "mmcif_url": "https://files.rcsb.org/download/4HHB.cif",
  "page_url": "https://www.rcsb.org/structure/4HHB",
  "pdb_id": "4HHB",
  "pdb_url": "https://files.rcsb.org/download/4HHB.pdb",
  "structure_factors_url": null
}

Get a structure's paper

Get the paper that describes a structure: title, journal, authors, abstract and subject headings, with links by DOI and on PubMed.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.

Outputs

abstracttext: The abstract, from PubMed
authorslist: The paper's authors
doitext: The paper's DOI
doi_urltext: A link to the paper by its DOI
journaltext: The journal, abbreviated
mesh_termslist: PubMed's MeSH subject headings
pagestext: Pages
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
pmc_idtext: Its free full text in PubMed Central, if any, such as PMC391849
publishedtrue/false: False while the paper is still 'To be published'
pubmed_idnumber: The paper's PubMed ID
pubmed_urltext: The paper on PubMed
titletext: The paper's title
volumetext: Journal volume
yearnumber: Year published

Example output

{
  "abstract": "The structure of human deoxyhaemoglobin was refined at 1.74 A resolution using data collected on film at room temperature from a synchrotron X-ray source. The crystallographic R-factor is 16.0%. The estimated error in atomic positions is 0.1 A overall, 0.14 A for main-chain atoms of internal segments, and 0.05 A for the iron atoms. The effects of intermolecular contacts on the structure were\u2026",
  "authors": [
    "Fermi, G.",
    "Perutz, M.F.",
    "Shaanan, B.",
    "Fourme, R."
  ],
  "doi": "10.1016/0022-2836(84)90472-8",
  "doi_url": "https://doi.org/10.1016/0022-2836(84)90472-8",
  "journal": "J Mol Biol",
  "mesh_terms": [
    "Crystallography",
    "Hemoglobins",
    "Humans",
    "Myoglobin"
  ],
  "pages": "159-174",
  "pdb_id": "4HHB",
  "pmc_id": null,
  "published": true,
  "pubmed_id": 6726807,
  "pubmed_url": "https://pubmed.ncbi.nlm.nih.gov/6726807/",
  "title": "The crystal structure of human deoxyhaemoglobin at 1.74 A resolution",
  "volume": "175",
  "year": 1984
}

Get an unreleased structure

Get a structure that has been deposited but not released: its title, when it was deposited, and why it is waiting, such as being held until its paper is published.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.

Outputs

authorslist: Who deposited it
deposit_datetext: When it was deposited (YYYY-MM-DD)
hold_untiltext: The date it is held until, if one was set (YYYY-MM-DD)
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
sequence_availabletrue/false: Whether its sequence is already public
statustext: Why it is not out yet, in words
status_codetext: The PDB's code, such as HPUB
titletext: The title the authors gave the structure

Example output

{
  "authors": [],
  "deposit_date": "2005-05-24",
  "hold_until": null,
  "pdb_id": "1ZSM",
  "sequence_available": false,
  "status": "Withdrawn by the authors",
  "status_code": "WDRN",
  "title": "Crystal Structure of the Catalytic Domain of Coagulation Factor XI in complex with 1-(2-Nitro-phenyl)-1H-indole-3-carboxamidine"
}

Get several structures

Get up to 100 structures in one step, each with its title, method, resolution, release date, organisms and paper. IDs the PDB does not have are listed separately.

Inputs

PDB IDspdb_idslistRequired: Up to 100 structure IDs: a list from an earlier step, or IDs separated by commas, spaces or new lines, such as 4HHB, 1CRN.

Outputs

countnumber: How many came back in this step
entrieslist: The structures found, in the order asked
not_foundlist: IDs the PDB has no released structure for

Example output

{
  "count": 2,
  "entries": [
    {
      "doi": "10.1016/0022-2836(84)90472-8",
      "experimental_method": "X-ray",
      "keywords": "OXYGEN TRANSPORT",
      "molecular_weight_kda": 64.74,
      "organisms": [
        "Homo sapiens"
      ],
      "pdb_id": "4HHB",
      "pubmed_id": 6726807,
      "release_date": "1984-07-17",
      "resolution_angstrom": 1.74,
      "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION",
      "url": "https://www.rcsb.org/structure/4HHB"
    },
    {
      "doi": "10.1073/pnas.81.19.6014",
      "experimental_method": "X-ray",
      "keywords": "PLANT PROTEIN",
      "molecular_weight_kda": 4.74,
      "organisms": [
        "Crambe hispanica subsp. abyssinica"
      ],
      "pdb_id": "1CRN",
      "pubmed_id": 16593516,
      "release_date": "1981-07-28",
      "resolution_angstrom": 1.5,
      "title": "WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION. PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN",
      "url": "https://www.rcsb.org/structure/1CRN"
    }
  ],
  "not_found": [
    "0ZZZ"
  ]
}

Get UniProt details for a molecule

Get the UniProt protein a molecule in a structure matches: its accession, name, function, genes, organism, full sequence, keywords and Gene Ontology terms.

Inputs

PDB IDpdb_idtextRequired: The structure's four-character ID, such as 4HHB for human hemoglobin. Lower case and rcsb.org links work too.
Moleculemolecule_idtextRequired: Which molecule in the structure: each different protein, DNA or RNA has a number, starting at 1, shared by all its copies. Fill in **PDB ID** first to pick from its molecules.

Outputs

countnumber: How many came back in this step
molecule_idtext: The molecule's number in the structure
pdb_idtext: The structure's four-character PDB ID, such as 4HHB
proteinslist: The UniProt proteins matched to the molecule

Example output

{
  "count": 1,
  "molecule_id": "1",
  "pdb_id": "4HHB",
  "proteins": [
    {
      "entry_name": "HBA_HUMAN",
      "function": "Involved in oxygen transport from the lung to the various peripheral tissues.",
      "genes": [
        "HBA1",
        "HBA2"
      ],
      "go_terms": [
        {
          "id": "GO:0005833",
          "name": "hemoglobin complex"
        },
        {
          "id": "GO:0031838",
          "name": "haptoglobin-hemoglobin complex"
        },
        {
          "id": "GO:0042744",
          "name": "hydrogen peroxide catabolic process"
        },
        {
          "id": "GO:0016020",
          "name": "membrane"
        }
      ],
      "keywords": [
        "3D-structure",
        "Acetylation",
        "Direct protein sequencing",
        "Disease variant"
      ],
      "length": 142,
      "organism": "Homo sapiens",
      "other_accessions": [
        "P01922",
        "Q1HDT5",
        "Q3MIF5",
        "Q53F97"
      ],
      "protein_name": "Hemoglobin subunit alpha",
      "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
      "taxonomy_id": 9606,
      "uniprot_id": "P69905",
      "url": "https://www.uniprot.org/uniprotkb/P69905/entry"
    }
  ]
}

Search structures

Search every structure's titles, descriptions, keywords, authors and papers for words, such as a protein, a disease or a gene, and get each match's title, method, resolution and organisms.

Inputs

Search forquerytextRequired: Words to look for, such as hemoglobin, spike protein or CDK2 inhibitor.
Include computed modelsinclude_computedtrue/false: Also search predicted structures from AlphaFold DB and ModelArchive. Off finds experimental structures only.Default: false.
Sort bysorttext: The order to list structures in.One of: relevance (Best match first), newest (Newest first), oldest (Oldest first), resolution (Sharpest resolution first). Default: relevance.
Max resultsmax_resultsnumber: Return at most this many results.From 1 to 100. Default: 10.
Skipskipnumber: Leave out this many results from the start, to get the next page. With Max results at 10, a Skip of 10 gives results 11 to 20.From 0 to 10000. Default: 0.

Outputs

countnumber: How many came back in this step
has_moretrue/false: Whether more results are left after these (raise Skip to get them)
querytext: What was searched for
resultslist: The structures found
totalnumber: How many match in all, across every page

Example output

{
  "count": 2,
  "has_more": true,
  "query": "hemoglobin",
  "results": [
    {
      "doi": "10.1006/jmbi.1994.1751",
      "experimental_method": "X-ray",
      "keywords": "OXYGEN TRANSPORT",
      "molecular_weight_kda": 64.71,
      "organisms": [
        "Sus scrofa"
      ],
      "pdb_id": "2PGH",
      "pubmed_id": 7990139,
      "release_date": "1994-11-30",
      "resolution_angstrom": 2.8,
      "score": 1.0,
      "title": "STRUCTURE DETERMINATION OF AQUOMET PORCINE HEMOGLOBIN AT 2.8 ANGSTROM RESOLUTION",
      "url": "https://www.rcsb.org/structure/2PGH"
    },
    {
      "doi": "10.1107/S0907444911006044",
      "experimental_method": "X-ray",
      "keywords": "OXYGEN TRANSPORT",
      "molecular_weight_kda": 32.49,
      "organisms": [
        "Canis lupus familiaris"
      ],
      "pdb_id": "3PEL",
      "pubmed_id": 21543841,
      "release_date": "2010-11-03",
      "resolution_angstrom": 1.9,
      "score": 0.9993,
      "title": "Structure of Greyhound Hemoglobin: Origin of High Oxygen Affinity",
      "url": "https://www.rcsb.org/structure/3PEL"
    }
  ],
  "total": 9220
}

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Search structures