aurekaresearch/opendde-harness/pdb-lookup

PDB lookup

Fixed, keyless endpoints. Fetch them with web_fetch (JSON comes back as is); never web-search for a PDB ID when one of these answers directly.

Find entries

Search API, GET with the query as URL-encoded JSON in ?json=:

https://search.rcsb.org/rcsbsearch/v2/query?json={"query":{"type":"terminal","service":"full_text","parameters":{"value":"PD-1 pembrolizumab"}},"return_type":"entry","request_options":{"paginate":{"start":0,"rows":10}}}

Returns result_set[].identifier (PDB IDs) with scores. Useful services: full_text (free text), text with attribute (e.g. rcsb_entity_source_organism.taxonomy_lineage.name, struct.title), sequence ({"value":"<sequence>","identity_cutoff":0.9,"evalue_cutoff":0.1,"sequence_type":"protein"}). return_type can be entry or polymer_entity.

Read one entry

https://data.rcsb.org/rest/v1/core/entry/5GGS

Read struct.title, exptl[].method, rcsb_entry_info.resolution_combined, rcsb_entry_info.polymer_entity_count, citation[0] (title, journal, year, pdbx_database_id_DOI), rcsb_entry_container_identifiers.polymer_entity_ids.

Per chain: https://data.rcsb.org/rest/v1/core/polymer_entity/5GGS/1 gives entity_poly.pdbx_seq_one_letter_code (sequence), rcsb_polymer_entity.pdbx_description, rcsb_entity_source_organism[].scientific_name and rcsb_polymer_entity_container_identifiers.auth_asym_ids (chain letters).

Sequences and coordinates

https://www.rcsb.org/fasta/entry/5GGS          # FASTA, one record per entity with chain letters
https://files.rcsb.org/download/5GGS.cif       # mmCIF coordinates (large: use bash + curl -o to save it)
https://files.rcsb.org/download/5GGS.pdb       # legacy PDB format when available

Keep results small

Ask the Data API only for the entry or entity you need, and quote the fields above rather than the whole document. A structure question is usually answered by one search plus one entry read.