/rcsb/entries/assemblies

POST /api/rcsb/entries/assemblies

Price: 1 credit

Get the biological assemblies of a PDB structure, with their composition and symmetry

How to use it

An assembly is the biologically meaningful form of the structure, which is often not what the deposited coordinates contain: a crystal asymmetric unit may hold half a dimer or several copies of it, and the operations here are what build the real one. Most entries have exactly one; where several are listed they are alternative proposals, and `is_candidate_assembly` marks the ones RCSB considers likely.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• entry string required — Four-character PDB identifier, or an RCSB structure URL containing one (examples: "4HHB", "https://www.rcsb.org/structure/6M0J"; minLength: 1)
• count integer required — Max number of results (min: 1; max: 200)

Response

• @type string (default: "RcsbAssembly")
• id string (default: "")
• entry_id string (default: "")
• assembly_id string (default: "")
• details string (default: "")
• rcsb_details string (default: "")
• method_details string (default: "")
• oligomeric_count integer nullable
• oligomeric_details string (default: "")
• is_candidate_assembly boolean nullable
• polymer_composition string (default: "")
• selected_polymer_entity_types string (default: "")
• na_polymer_entity_types string (default: "")
• formula_weight number nullable
• atom_count integer nullable
• polymer_atom_count integer nullable
• nonpolymer_atom_count integer nullable
• branched_atom_count integer nullable
• solvent_atom_count integer nullable
• hydrogen_atom_count integer nullable
• deuterated_water_count integer nullable
• polymer_monomer_count integer nullable
• modeled_polymer_monomer_count integer nullable
• unmodeled_polymer_monomer_count integer nullable
• polymer_entity_count integer nullable
• protein_entity_count integer nullable
• dna_entity_count integer nullable
• rna_entity_count integer nullable
• nucleic_acid_entity_count integer nullable
• nucleic_acid_hybrid_entity_count integer nullable
• nonpolymer_entity_count integer nullable
• branched_entity_count integer nullable
• solvent_entity_count integer nullable
• polymer_entity_instance_count integer nullable
• protein_entity_instance_count integer nullable
• dna_entity_instance_count integer nullable
• rna_entity_instance_count integer nullable
• nucleic_acid_entity_instance_count integer nullable
• nucleic_acid_hybrid_entity_instance_count integer nullable
• nonpolymer_entity_instance_count integer nullable
• branched_entity_instance_count integer nullable
• solvent_entity_instance_count integer nullable
• interface_count integer nullable
• interface_entity_count integer nullable
• homomeric_interface_entity_count integer nullable
• heteromeric_interface_entity_count integer nullable
• isologous_interface_entity_count integer nullable
• heterologous_interface_entity_count integer nullable
• protein_interface_entity_count integer nullable
• nucleic_acid_interface_entity_count integer nullable
• protein_nucleic_acid_interface_entity_count integer nullable
• buried_surface_area number nullable
• interface_residue_count integer nullable
• interface_ids array (default: [])
• symmetry_provenance_code string (default: "")
• symmetries array (default: [])
  • @type string (default: "RcsbSymmetry")
  • kind string (default: "")
  • type string (default: "")
  • symbol string (default: "")
  • stoichiometry array (default: [])
  • oligomeric_state string (default: "")
  • clusters array (default: [])
    • @type string (default: "RcsbSymmetryCluster")
    • average_rmsd number nullable
    • member_chain_ids array (default: [])
    • member_operation_ids array (default: [])
  • rotation_axes array (default: [])
    • @type string (default: "RcsbRotationAxis")
    • order integer nullable
    • start array (default: [])
    • end array (default: [])
• symmetry_lineage array (default: [])
  • @type string (default: "RcsbLineageNode")
  • id string (default: "")
  • name string (default: "")
  • depth integer nullable
• evidence array (default: [])
  • @type string (default: "RcsbAssemblyEvidence")
  • experimental_support string (default: "")
  • details string (default: "")
• generations array (default: [])
  • @type string (default: "RcsbAssemblyGeneration")
  • assembly_id string (default: "")
  • chain_ids array (default: [])
  • operator_expression string (default: "")
• operations array (default: [])
  • @type string (default: "RcsbAssemblyOperation")
  • id string (default: "")
  • name string (default: "")
  • type string (default: "")
  • symmetry_operation string (default: "")
  • matrix array (default: [])
  • vector array (default: [])

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — Entry not found Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.