Data Rcsb RCSB RESTful API

Name: RCSB RESTful API
Brand: RCSB RESTful API
Availability: InStock

★ Only Publicly Available OpenAPI DocumentHealthcareClinical Datanone39 EndpointsREST

For Agents

Retrieve protein structures, chemical components, polymer entities, interfaces, and groups from the RCSB Protein Data Bank for research and drug discovery workflows.

Install Jentic One Beta

Connect the RCSB RESTful API to your agent

Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the RCSB RESTful API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.

Two steps, two machines. Install the instance in a safe environment, then register your agent from wherever it runs.

Step 1: Jentic One Host machine

# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh

Step 2: Agent machine

# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register       # connects your agent to your Jentic One instance

Jentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.

Capabilities

What an agent can do with RCSB RESTful API.

Retrieve a structure entry by PDB entry ID

Fetch assembly descriptions for a given entry and assembly ID

Retrieve polymer, non-polymer, and branched entity records by entry and entity ID

GET STARTED

Start building with RCSB RESTful API

Explore with Jentic

View OpenAPI Document

Jentic publishes the only available OpenAPI specification for the RCSB RESTful API, keeping it validated and agent-ready. The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank exposes structured access to the canonical archive of three-dimensional macromolecular structures used in life sciences research and drug discovery. The 39-endpoint API covers entries, assemblies, polymer and non-polymer entities, entity instances, chemical components, interfaces, groups, schema, and repository holdings. Endpoints are public and require no authentication.

Use Cases

Patterns agents use RCSB RESTful API for, with concrete tasks.

★ Structure Retrieval for Drug Discovery

Pull protein structure metadata directly from the canonical PDB archive when running computational drug discovery pipelines. GET /core/entry/{entry_id} returns the entry, and GET /core/assembly/{entry_id}/{assembly_id} returns the biological assembly detail. Suitable for research teams in pharma, biotech, and academic labs that need programmatic access to PDB entries.

Fetch the PDB entry '6VXX' via GET /core/entry/{entry_id} and its assembly 1 via GET /core/assembly/{entry_id}/{assembly_id} and return the title and resolution.

Ligand and Chemical Component Lookups

Resolve chemical component identifiers to their full RCSB record including DrugBank annotations. GET /core/chemcomp/{comp_id} returns the chemical component definition, and GET /core/drugbank/{comp_id} returns DrugBank-derived annotations when available. Useful for cheminformatics workflows mapping ligands to drugs.

Look up CCD ID 'ATP' via GET /core/chemcomp/{comp_id} and return the chemical name, formula, and any DrugBank annotations from GET /core/drugbank/{comp_id}.

Interface and Entity Analysis

Drive interface analysis pipelines by retrieving pairwise polymeric interfaces and the polymer entities they connect. GET /core/interface/{entry_id}/{assembly_id}/{interface_id} returns the interface description, while polymer entity endpoints provide entity-level metadata. Useful for structural biology teams studying protein-protein interactions.

Retrieve the interface description for entry '1A2K' assembly 1 interface 1, then fetch the polymer entities involved to summarise the interaction.

Group-Based Aggregation Queries

Aggregate structures by deposition group or non-polymer entity group to study related entries together. GET /core/entry_groups/{group_id} returns entries by PDB Group Deposition ID, and GET /core/nonpolymer_entity_groups/{group_id} returns non-polymer entities grouped by chemical component. Useful for structural genomics consortia and curation teams.

Fetch the entry group for a PDB Group Deposition ID and produce a list of member entry IDs with their resolutions.

Agent-Driven Structural Biology Tools via Jentic

AI agents that draft research summaries or feed structure data into modelling tools can call RCSB through Jentic without managing endpoint URLs by hand. The agent searches Jentic for the relevant intent, loads the schema, and executes entry, assembly, or chemical component lookups. The endpoints are public, so Jentic mediates discovery and parameter shaping.

Use Jentic to search 'get a pdb entry', load GET /core/entry/{entry_id}, and execute it with the entry ID supplied by the user.

Key Endpoints

39 endpoints — jentic publishes the only available openapi specification for the rcsb restful api, keeping it validated and agent-ready.

METHOD

PATH

DESCRIPTION

GET

/core/entry/{entry_id}

Get a structure entry by entry ID

GET

/core/assembly/{entry_id}/{assembly_id}

Get a structural assembly by entry and assembly ID

GET

/core/chemcomp/{comp_id}

Get a chemical component by CCD ID

GET

/core/drugbank/{comp_id}

Get DrugBank annotations for a chemical component

GET

/core/interface/{entry_id}/{assembly_id}/{interface_id}

Get a pairwise polymeric interface description

GET

/core/entry_groups/{group_id}

Get an aggregated entry group

GET

/core/branched_entity/{entry_id}/{entity_id}

Get a branched entity by entry and entity ID

GET

/core/entry/{entry_id}

Get a structure entry by entry ID

GET

/core/assembly/{entry_id}/{assembly_id}

Get a structural assembly by entry and assembly ID

GET

/core/chemcomp/{comp_id}

Get a chemical component by CCD ID

GET

/core/drugbank/{comp_id}

Get DrugBank annotations for a chemical component

GET

/core/interface/{entry_id}/{assembly_id}/{interface_id}

Get a pairwise polymeric interface description

Why Jentic?

Three things that make agents converge on Jentic-routed access.

Credential isolation

RCSB endpoints are unauthenticated. Jentic still routes calls through its execution layer so agents benefit from consistent retry, logging, and rate-limit handling alongside other authenticated APIs in the same workflow.

Intent-based discovery

Agents search by intent (e.g. 'get a pdb entry') and Jentic returns the matching GET /core/entry/{entry_id} operation with its input schema, so the agent calls the right endpoint without parsing the RCSB Redoc reference.

Time to first call

Direct RCSB integration: 1-2 days to model the 39-endpoint surface. Through Jentic: under 30 minutes — search, load, execute.

FAQs

Specific to using RCSB RESTful API through Jentic.

Why is there no official OpenAPI spec for the RCSB RESTful API?

RCSB publishes a Redoc-rendered API doc but not a structured OpenAPI specification. Jentic generates and maintains this spec so that AI agents and developers can call the RCSB RESTful API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.

What authentication does the RCSB RESTful API use?

The RCSB RESTful API is fully public and requires no authentication. Jentic still routes calls through its execution layer so agents benefit from consistent rate-limiting, retries, and logging across providers.

Can I retrieve a PDB entry by ID with this API?

Yes. GET /core/entry/{entry_id} returns the structure record for the supplied PDB entry ID, and the related GET /core/assembly/{entry_id}/{assembly_id} endpoint returns the biological assembly detail.

What are the rate limits for the RCSB RESTful API?

RCSB does not publish hard rate limits but advises avoiding sustained high-frequency requests against the public service. Apply client-side caching of entry records and exponential backoff on 429 or 503 responses for batch jobs.

How do I look up a chemical component through Jentic?

Run pip install jentic, then search Jentic for 'look up a chemical component', load the GET /core/chemcomp/{comp_id} schema, and execute it with the CCD ID. Pair with GET /core/drugbank/{comp_id} for DrugBank annotations.

Does the RCSB RESTful API support interface and entity instance lookups?

Yes. GET /core/interface/{entry_id}/{assembly_id}/{interface_id} returns pairwise polymeric interface descriptions and the entity-instance endpoints return descriptions keyed by entry ID and asym ID for polymer, non-polymer, and branched entities.