RCSB PDB website screenshot

RCSB PDB

RCSB Protein Data Bank (RCSB PDB) is a scientific data resource providing free, open access to the 3D structural data of biological macromolecules including proteins, nucleic acids, and complex assemblies. It serves researchers worldwide through a suite of programmatic APIs covering data retrieval, full-text and attribute search, sequence and structure similarity search, molecular model data access, volumetric electron density maps, sequence coordinate alignments, and structure alignment calculations.

RCSB PDB publishes 4 APIs on the APIs.io network, including General API, Metadata Service API, Search Service API, and 1 more. Tagged areas include Structural Biology, Proteomics, Bioinformatics, Genomics, and Life Sciences.

RCSB PDB’s developer surface includes documentation, getting-started guide, GitHub presence, and 13 more developer resources.

🌐 Visit website 📡 Source on GitHub
30.5/100 thin ▬ flat Agent 32/100 agent aware Full breakdown ↓
scored 2026-07-28 · rubric v0.6
AccessFree
7 APIs
Structural BiologyProteomicsBioinformaticsGenomicsLife SciencesOpen DataResearchMacromoleculesCrystallographyNMR

Kin Score

Kin Score Kin Score How this is scored →
scored 2026-07-28 · rubric v0.6
Composite quality — 30.5/100 · thin
Contract Quality 10.6 / 25
Developer Ergonomics 3.9 / 20
Commercial Clarity 5.8 / 20
Operational Transparency 6.8 / 13
Governance 0.0 / 12
Discoverability 7.4 / 10
Agent readiness — 32/100 · agent aware
Machine-Readable Contract 18 / 18
Agentic Access Contract 10 / 10
MCP Server 0 / 12
Machine-Readable Auth 0 / 10
Idempotency 0 / 9
Stable Error Semantics 8 / 8
Request/Response Examples 7 / 7
Rate-Limit Signaling 7 / 7
Typed Event Surface 0 / 6
Agent Skills 0 / 5
Well-Known Catalog 0 / 4
Consent & Bot Identity 0 / 3
A2A Agent Card 0 / 8
Dry-Run / Simulate Mode 0 / 4
Improve this rating by publishing the missing artifacts — every area above can be raised, and the full rubric is at apis.io/rating/. This rating is computed from github.com/api-evangelist/pdb: open an issue to ask a question, or submit a pull request to add artifacts. Want it done for you? Prioritized profiling — $2,500 →

APIs 7

Individual APIs this provider publishes, each with its own machine-readable definition.

RCSB PDB Data API

Provides structured access to the complete RCSB PDB holdings via REST and GraphQL interfaces. Given a known PDB identifier, callers can retrieve rich JSON metadata about entries...

RCSB PDB Sequence Coordinates API

GraphQL service providing sequence-level alignments between structural databases and external sequence resources. Exposes two core queries — alignment and annotations — enabling...

RCSB PDB Structure Alignment API

Asynchronous REST API that performs programmatic structure alignment calculations between PDB entries or user-supplied coordinate files. Callers submit an alignment job via POST...

RCSB PDB General API

The General API from RCSB PDB — 12 operation(s) for general.

RCSB PDB Metadata Service API

The Metadata Service API from RCSB PDB — 3 operation(s) for metadata service.

RCSB PDB Search Service API

The Search Service API from RCSB PDB — 2 operation(s) for search service.

RCSB PDB Suggest Service API

The Suggest Service API from RCSB PDB — 1 operation(s) for suggest service.

Scroll for all 7

GraphQL 1

GraphQL schemas published by this provider.

RCSB Protein Data Bank GraphQL API

The RCSB PDB GraphQL API provides flexible, field-selective access to the complete structural biology holdings of the Protein Data Bank. Callers can retrieve richly nested metad...

GRAPHQL

Pricing Plans 1

Published pricing tiers and plan structures.

Pdb Plans Pricing

1 plans

PLANS

Rate Limits 1

Documented rate limits and quota policies.

Pdb Rate Limits

7 limits

RATE LIMITS

FinOps 1

Cost, billing, and metering signals for API financial operations.

Pdb Finops

FINOPS

Security Posture 1

Authentication, domain security, vulnerability disclosure, and trust-center signals.

Pdb Domain Security

TLSv1.3 · HSTS · DMARC

SECURITY

Agentic Access 1

Recommended x-agentic-access execution contracts for AI agents.

Pdb Agentic Access

28 operations · 10 acting

28 operations · 10 acting

AGENTIC

Resources

Get Started 1

Portal, sign-up, and the first successful call

GettingStarted
GettingStarted

Documentation 1

Reference material describing how the API behaves

Documentation
Documentation

Agent Surfaces 1

MCP servers, agent skills, and machine-readable catalogs

AgenticAccess
AgenticAccess

Design & Contract 1

Pagination, idempotency, versioning, errors, and events

JSONLD
JSONLD

Build 3

SDKs, sample code, and the tooling you integrate with

GitHub
GitHub
 PythonSDK
PythonSDK
 JavaScriptSDK
JavaScriptSDK

Access & Security 1

Authentication, authorization, and security posture

DomainSecurity
DomainSecurity

Operate 3

Status, limits, changes, and where to get help

StatusPage
StatusPage
 RateLimits
RateLimits
 Contact
Contact

Commercial 2

Pricing, plans, and the legal terms of use

Plans
Plans
 FinOps
FinOps

Company 1

The organization behind the API

Website
Website

Other 2

Properties that don't map to a standard resource type

FileDownloads
FileDownloads
 MailingList
MailingList

Source (apis.yml)

apis.yml Raw ↑ 
aid: pdb
name: RCSB PDB
description: RCSB Protein Data Bank (RCSB PDB) is a scientific data resource providing free, open access to the 3D structural
  data of biological macromolecules including proteins, nucleic acids, and complex assemblies. It serves researchers worldwide
  through a suite of programmatic APIs covering data retrieval, full-text and attribute search, sequence and structure similarity
  search, molecular model data access, volumetric electron density maps, sequence coordinate alignments, and structure alignment
  calculations.
accessModel:
  pricing: free
  onboarding: unknown
  trial: false
  try_now: false
  public: false
  label: Free
  confidence: medium
  source:
  - plans
  generated: '2026-07-22'
  method: derived
image: https://www.rcsb.org/img/rcsb_logo.png
url: https://raw.githubusercontent.com/api-evangelist/pdb/refs/heads/main/apis.yml
humanURL: https://www.rcsb.org
baseURL: https://data.rcsb.org
tags:
- Structural Biology
- Proteomics
- Bioinformatics
- Genomics
- Life Sciences
- Open Data
- Research
- Macromolecules
- Crystallography
- NMR
created: '2026-06-13'
modified: '2026-06-13'
specificationVersion: '0.19'
type: Index
position: Producer
access: Open
apis:
- aid: pdb:rcsb-pdb-data-api
  name: RCSB PDB Data API
  description: Provides structured access to the complete RCSB PDB holdings via REST and GraphQL interfaces. Given a known
    PDB identifier, callers can retrieve rich JSON metadata about entries, polymer entities, non-polymer entities (ligands),
    polymer entity instances (chains), assemblies, branched entities, and chemical components. The REST surface mirrors an
    OpenAPI/ReDoc contract while the GraphQL endpoint supports flexible field selection and nested queries.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Structural Biology
  - Protein Data
  - GraphQL
  - REST
  - JSON
  properties:
  - type: Documentation
    url: https://data.rcsb.org/redoc/index.html
  - type: GraphQL
    url: https://data.rcsb.org/graphql
  - type: GraphQLExplorer
    url: https://data.rcsb.org/graphiql/index.html
  - type: PythonSDK
    url: https://github.com/rcsb/py-rcsb-api
  - type: JavaScriptSDK
    url: https://github.com/rcsb/rcsb-api-tools
  - type: GraphQLSchema
    url: graphql/pdb-schema.graphql
  - type: GraphQLDocumentation
    url: graphql/pdb-graphql.md
  contact:
  - type: Email
    url: mailto:info@rcsb.org
  - type: MailingList
    url: mailto:api+subscribe@rcsb.org
- aid: pdb:rcsb-pdb-sequence-coordinates-api
  name: RCSB PDB Sequence Coordinates API
  description: GraphQL service providing sequence-level alignments between structural databases and external sequence resources.
    Exposes two core queries — alignment and annotations — enabling callers to map PDB chain positions to UniProt, NCBI RefSeq
    (protein and genomic), CATH, SCOPe, and Computed Structure Models (CSMs). Replaces the legacy 1D Coordinates Service.
  humanURL: https://sequence-coordinates.rcsb.org
  baseURL: https://sequence-coordinates.rcsb.org/graphql
  tags:
  - Sequence Alignment
  - UniProt
  - NCBI
  - GraphQL
  - Annotations
  properties:
  - type: Documentation
    url: https://sequence-coordinates.rcsb.org
  - type: GraphQLExplorer
    url: https://sequence-coordinates.rcsb.org/graphiql/index.html
  contact:
  - type: Email
    url: mailto:info@rcsb.org
- aid: pdb:rcsb-pdb-alignment-api
  name: RCSB PDB Structure Alignment API
  description: Asynchronous REST API that performs programmatic structure alignment calculations between PDB entries or user-supplied
    coordinate files. Callers submit an alignment job via POST /submit (accepting PDBx/mmCIF, BinaryCIF, or legacy PDB format,
    with optional gzip compression), receive a UUID ticket, and poll GET /results for status and output. Enables large-scale
    structural comparison workflows without manual interaction with the RCSB PDB website.
  humanURL: https://alignment.rcsb.org
  baseURL: https://alignment.rcsb.org
  tags:
  - Structure Alignment
  - Structural Comparison
  - Asynchronous
  - Computational
  properties:
  - type: Documentation
    url: https://alignment.rcsb.org/api-reference.html
  - type: QueryEditor
    url: https://alignment.rcsb.org/query-editor.html
  contact:
  - type: Email
    url: mailto:info@rcsb.org
- aid: pdb:pdb-general-api
  name: RCSB PDB General API
  description: The General API from RCSB PDB — 12 operation(s) for general.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - General
  properties:
  - type: OpenAPI
    url: openapi/pdb-general-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-metadata-service-api
  name: RCSB PDB Metadata Service API
  description: The Metadata Service API from RCSB PDB — 3 operation(s) for metadata service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Metadata Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-metadata-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-search-service-api
  name: RCSB PDB Search Service API
  description: The Search Service API from RCSB PDB — 2 operation(s) for search service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Search Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-search-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
- aid: pdb:pdb-suggest-service-api
  name: RCSB PDB Suggest Service API
  description: The Suggest Service API from RCSB PDB — 1 operation(s) for suggest service.
  humanURL: https://data.rcsb.org
  baseURL: https://data.rcsb.org/rest/v1/core
  tags:
  - Suggest Service
  properties:
  - type: OpenAPI
    url: openapi/pdb-suggest-service-api-openapi.yml
  - type: Documentation
    url: https://search.rcsb.org/redoc/index.html
  - type: GettingStarted
    url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  - type: Documentation
    url: https://models.rcsb.org
  - type: Documentation
    url: https://maps.rcsb.org
common:
- type: AgenticAccess
  url: agentic-access/pdb-agentic-access.yml
- type: DomainSecurity
  url: security/pdb-domain-security.yml
- type: JSONLD
  url: json-ld/pdb.json
- type: Website
  url: https://www.rcsb.org
- type: Documentation
  url: https://www.rcsb.org/docs/programmatic-access/web-apis-overview
- type: GettingStarted
  url: https://www.rcsb.org/docs/programmatic-access
- type: FileDownloads
  url: https://files.wwpdb.org
- type: GitHub
  url: https://github.com/rcsb
- type: PythonSDK
  url: https://github.com/rcsb/py-rcsb-api
- type: JavaScriptSDK
  url: https://github.com/rcsb/rcsb-api-tools
- type: StatusPage
  url: https://www.rcsb.org/pages/policies
- type: RateLimits
  url: rate-limits/pdb-rate-limits.yml
- type: Plans
  url: plans/pdb-plans-pricing.yml
- type: FinOps
  url: finops/pdb-finops.yml
- type: Contact
  url: mailto:info@rcsb.org
- type: MailingList
  url: https://groups.google.com/g/rcsb-pdb-api-announcements
maintainers:
- FN: Kin Lane
  email: kin@apievangelist.com