/rcsb/polymer-entities/uniprot

POST /api/rcsb/polymer-entities/uniprot

Price: 10 credits

Get the UniProt records a polymer entity of a PDB structure maps to

How to use it

This is the curated bridge from a structure chain to UniProt, carrying the reference protein name, gene, full sequence, keywords and sequence features. Only protein entities have one, so a nucleic-acid chain answers 412, which means the mapping is absent rather than the entity. One entity can map to several accessions, which is why the answer is a list.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• polymer_entity string required — Polymer entity identifier such as 4HHB_1, or the PDB entry id when entity_id is given (examples: "4HHB_1", "4HHB"; minLength: 1)
• entity_id string nullable — Entity number inside the entry, required when polymer_entity carries only the entry id (examples: "1"; minLength: 1)
• count integer required — Max number of results (min: 1; max: 50)

Response

• @type string (default: "RcsbUniprotMapping")
• id string (default: "")
• accession string (default: "")
• entry_name string (default: "")
• protein_name string (default: "")
• gene_names array (default: [])
• ec_numbers array (default: [])
• function string (default: "")
• sequence string (default: "")
• organism_scientific_name string (default: "")
• organism_tax_id string (default: "")
• isoform_accessions array (default: [])
• reference_databases array (default: [])
• keywords array (default: [])
  • @type string (default: "RcsbUniprotKeyword")
  • id string (default: "")
  • name string (default: "")
• features array (default: [])
  • @type string (default: "RcsbUniprotFeature")
  • id string (default: "")
  • type string (default: "")
  • description string (default: "")
  • begin_sequence_position integer nullable
  • end_sequence_position integer nullable
• annotations array (default: [])
  • @type string (default: "RcsbAnnotation")
  • id string (default: "")
  • name string (default: "")
  • type string (default: "")
  • description string (default: "")
  • provenance_source string (default: "")
  • assignment_version string (default: "")
  • lineage array (default: [])
    • @type string (default: "RcsbLineageNode")
    • id string (default: "")
    • name string (default: "")
    • depth integer nullable
  • additional_properties array (default: [])
    • @type string (default: "RcsbNamedValues")
    • name string (default: "")
    • values array (default: [])
• external_references array (default: [])
  • @type string (default: "RcsbUniprotExternalReference")
  • name string (default: "")
  • id string (default: "")
  • provenance_source string (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 — Polymer entity not found, or it maps to no UniProt record 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.