Search experimental (PDB) and predicted (computed-model) protein structures by free text, protein sequence (triggers an mmseqs2 similarity search), and/or organism, method, and resolution filters. Returns ranked hits; the experimental page is enriched with title, method, resolution, and organism. Chain hit IDs into protein_get_structure. Optionally returns a facet breakdown (counts by method / organism / release year / …) alongside the hits at no extra call. A facet on a dimension you are already filtering (e.g. the organism facet while organism is set) lists unfiltered alternatives by design — it does not constrain by its own active filter, so you can see sibling values to pivot to. Numeric histogram buckets (resolution, molecular weight) carry explicit rangeFrom/rangeTo bounds so a boundary label is unambiguous.
Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call), and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source "predicted" with their modelling provider; "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); "best_available" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Records served by the RCSB entry endpoint also carry polymer entities with both chain namespaces (labelAsymIds for protein_compare_structures, authAsymIds for protein_get_annotations), bound ligands, molecular weight, and release date. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[], and IDs beyond the cap are reported in the notice. Set include_coords to inline coordinate content; if the inlined bytes exceed the response budget the content is withheld and overflow lists each structure's size — re-call with sections:[ids] for specific structures, or for a single oversized file download it from that record's coordinateUrls.
Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id and databases belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.
Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequency — most-deposited component first, so the top hit is the most common match for the name, not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only (computed from deposited coordinates; predicted models carry no bound ligands).
Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's modeled-residue count and alignment coverage. TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.
Profile the PDB into distributions and trends over an optional scoping query: counts by method, organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs server-side at RCSB — one call returns compact buckets, no row pull. Pass one group_by dimension for a single breakdown, or two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension level separately rather than the response, so a cross-tab returns up to that many nested buckets under each of its capped parent buckets; bucketsReturned reports the realized total.
Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries an "attribution" block with the upstream data licenses and citations.