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 7 API contracts indexed on the APIs.io network, including General API, Metadata Service API, Search Service API, and 4 more. Tagged areas include Structural Biology, Proteomics, Bioinformatics, Genomics, and Life Sciences.

The RCSB PDB catalog on APIs.io includes 1 Spectral governance ruleset.

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

🌐 Visit website 📡 Profile data on GitHub

28.2/100 thin ▬ flat Agent 23/100 agent aware Front door AI 1/6 silent Heartbeat 91/100 alive saas Full breakdown ↓
scored 2026-11-06 · rubric v0.27.0 · Show this score on your site →

AccessFree

3 published contracts

Structural Biology Proteomics Bioinformatics Genomics Life Sciences Open Data ResearchMacromoleculesCrystallographyNMRResearch Data

Kin Score

Kin Score How this is scored →
scored 2026-11-06 · rubric v0.27.0

Composite quality — 28.2/100 · thin

Contract Quality 7.6 / 19

Developer Ergonomics 3.6 / 15

Access Clarity 2.0 / 15

Operational Transparency 2.8 / 10

Contract Governance 1.2 / 9

Discoverability 5.4 / 8

Regulatory Posture 0.7 / 15

Create-or-Update Ergonomics 0.0 / 10

Agent readiness — 23/100 · agent aware

Machine-Readable Contract 18 / 18

Agentic Access Contract 10 / 10

Documented Reversibility 0 / 6

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

Delegated User Identity 0 / 6

Protected Resource Metadata 0 / 5

Registration Without a Human 0 / 6

Agentic Commerce Well-Known Document 0 / 5

Pagination 5 / 5

Distinct Operations 0 / 3

MCP Tool Quality 6 / 6

Regulatory Posture applies to this provider. Its tags matched the Health regime, so Regulatory Posture carries 15 points of the composite. If this regime is wrong for your business, say so on your provider repo — the applicability map is public and we will correct it.

Create-or-Update Ergonomics applies to this provider. This API accepts writes, so it carries 10 points of the composite. It is scored from the published contracts themselves: whether a caller can create-or-update in one call, whether the write accepts a key the caller already holds, and whether the response says which branch ran. Without that, every write needs a search-and-branch in front of it, and the first time that check is skipped a duplicate record is created. Scored against the observed mean rather than raw — a provider at the catalog average is unchanged by this facet, not penalised by it.

The six quality facets above are damped to 75 points between them, because the conditional facet above carries the other 25. That is why each facet's contribution is shown against a damped maximum: raising a quality facet moves the composite by 75% of its nominal weight, not 100%. The full arithmetic is at apis.io/rating/.

Show this score on your site.

It updates itself when the score changes. Paste this where you link to your API docs:

<a href="https://apis.io/providers/pdb/"><img src="https://apis.io/badge/pdb/card.svg" alt="RCSB PDB on APIs.io — Kin Score by API Evangelist"></a>

Other styles, a README pill and a shields.io endpoint are on the badge page.

Raise your score.

Agent readiness — checks not met, largest first (exact, from this profile):

MCP Server +12 pts — deployment.mode + probe verdict on the mcp/ manifest, not the pointer; an unprobed slug falls back to authorship
Machine-Readable Auth +10 pts — a served openid-configuration/oauth-authorization-server carrying `issuer` (served), else the securitySchemes class in the provider OpenAPIs — bound (mutualTLS, DPoP, Signature) > negotiable (oauth2 authorizationCode/clientCredentials, openIdConnect) > bearer (http bearer, apiKey)
Idempotency +9 pts — OpenAPI mutating operations declare an idempotency key — a header, a request-body property, or a named de-duplication token whose own description says so (verified); else common[].type matches /idempoten/i (documented)
A2A Agent Card +8 pts — a2a/-a2a.yml manifest, graded on conformance.grade against A2A 1.0.0
Registration Without a Human +6 pts — a `registration_endpoint` in the served RFC 8414 / OIDC discovery document
Delegated User Identity +6 pts — a served discovery document listing authorization_code in grant_types_supported (served), else an oauth2 authorizationCode flow or openIdConnect declared in an OpenAPI (documented)

9 more unmet checks in the Agent Readiness table above.

Kin Score — facets with the most composite points still available (weight × headroom):

Access Clarity scores 13.2 — up to +17.4 composite points
Developer Ergonomics scores 23.8 — up to +15.2 composite points
Contract Quality scores 40.3 — up to +14.9 composite points

Each check links to what satisfies it. Publish the artifact, or tell us where it already lives, and the score moves on the next scoring run.

Improve this rating by publishing the missing artifacts — every area above can be raised, and the full rubric is at apis.io/rating/. Every facet and dimension name above is a link: it opens that measurement's own page — what it means, the exact checks that feed it, how the whole catalog distributes on it, and the providers at the top of it. This rating is computed from the provider profile at artifacts.apis.io/pdb/apis.yml: open an issue on github.com/api-evangelist/pdb to ask a question or point us at an artifact you publish. Submit an artifact on GitHub — free → Manage your own listing — the Influence plan, $499/mo →

Markets this provider is in provisional

The Kin Score Market layer reads a provider inside its market: its position, and how deep its integrations go. Depth is only comparable within a position. Provisional and unweighted: not part of the Kin Score or agent readiness.

Market	Position	Depth	Registered MCP server	Declares compatibility
Raycast Store Extensions (first-party publishers + community-wrapped products)	covered	9.6 (thin)	-	-

Registered MCP server and declares compatibility are report only — not weighted. Undeclared means we found nothing we can read, so there is no number: we never infer integrations.

Standards implemented 1

Standards this provider implements or carries. De facto ones are profiled and measured by the API Commons; formal ones come from the standards directory and are linked by the provider's own tags. The evidence column says how each claim was established — not that it was made.

OpenAPI

measured — observed by APIs.io (published)

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

Open Collections 4

Open, tool-agnostic API collections (OpenAPI-derived and Bruno).

ModelServer General API

OPEN COLLECTION

ModelServer General Metadata Service API

OPEN COLLECTION

ModelServer General Search Service API

OPEN COLLECTION

ModelServer General Suggest Service API

OPEN COLLECTION

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

RCSB PDB API pricing

Not yet checked against RCSB PDB's own pricing page. Compiled by API Evangelist on 2026-06-13 from www.rcsb.org/docs/programmatic-access/web-apis-overview; confirm before you rely on a figure. A free plan or tier is listed.

Plan	Price
Open Access open	Free

Plan details, limits and sources →

Rate limits

Data API Default: 10 requests per second
Search API Default: 10 requests per second
ModelServer API Default: 10 requests per second

Compiled by API Evangelist, not yet checked against RCSB PDB's documentation. All 7 limits →

Billed by: request · FinOps profile →

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

Service Levels 1

Uptime the provider promises or reports, as SLA4OAI. Read from its own pages; APIs.io runs no monitors.

RCSB PDB

SLA

FinOps 1

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

Pdb Finops

FINOPS

Spectral Rules 1

Spectral governance rulesets for linting and validating these APIs.

RCSB PDB API Rules

41 rules · 32 errors 7 warnings 2 info

SPECTRAL

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 · 9 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 2

The organization behind the API

Blog

Blog

Website

Website

Other 2

Properties that don't map to a standard resource type

FileDownloads

FileDownloads

MailingList

MailingList

Source (apis.yml)

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.
deliveryModel:
  model: saas
  open_source: false
  commercial: true
  callable_host: true
  label: Hosted service · you call their endpoint
  confidence: high
  source:
  - openapi
  - pricing
  generated: '2026-08-28'
  method: derived
accessModel:
  pricing: free
  onboarding: unknown
  trial: false
  try_now: false
  public: false
  label: Free
  confidence: low
  source:
  - plans
  - security
  generated: '2026-11-06'
  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
- Research Data
created: '2026-06-13'
modified: '2026-10-06'
specificationVersion: '0.23'
type: Index
position: Producing
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
  - Annotation
  tags_raw:
  - 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: []
  tags_raw:
  - 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:
- url: https://www.rcsb.org/pages/news
  type: Blog
- 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

RCSB PDB API — frequently asked questions

Does RCSB PDB have an API?

Yes. APIs.io lists 7 APIs from RCSB PDB, including RCSB PDB Data API, RCSB PDB Sequence Coordinates API and RCSB PDB Structure Alignment API, and 4 more.

Is there an OpenAPI specification for the RCSB PDB API?

Yes. APIs.io indexes 4 OpenAPI specifications for RCSB PDB, each linked for download from this page.

How much does the RCSB PDB API cost?

APIs.io lists 1 pricing plan for RCSB PDB, with each plan's price, limits and inclusions under Pricing on this page.

Is the RCSB PDB API ready for AI agents?

RCSB PDB has a Kin Score of 28.2 out of 100 (thin) and an Agent Readiness score of 23.2 (agent-aware), scored by API Evangelist on 2026-11-06.

Work with this as data

Every provider here is available over the APIs.io API and to AI agents over MCP.

MCP server

One button, every client — Claude, Cursor, VS Code and the rest.

https://apis.io/mcp

Tools for providers

9 MCP tools reach this

find_providersBrowse and filter every provider in the catalog.
get_provider_artifactsEvery artifact this provider publishes, grouped by type.
get_provider_operationsEvery operation across all of their OpenAPIs — one call instead of parsing every spec.
get_provider_toolsEvery MCP tool they ship, with the operation each wraps.
get_provider_evidenceHow each part of their score was established. Free — the basis for a claim should not sit behind it.
get_provider_ratingPRO — composite, band, trend and facet scores.
apis_io_searchSTART HERE — APIs, providers and tags for one query, each with its total.
resolveTurn a domain, URL or GitHub org into the provider it belongs to.
find_cohortsEvery scored population of providers in the catalog.

All 92 tools →

Call it yourself

curl for this page

This provider

curl "https://apis.io/api/v1/providers/pdb"

All providers

curl "https://apis.io/api/v1/providers?limit=25"

Every operation they expose

curl "https://apis.io/api/v1/providers/pdb/operations?limit=25"

How their score was established

curl "https://apis.io/api/v1/providers/pdb/evidence"

Calls without X-API-Key need no key. Calls with it need a paid plan — get a key.

Get an API key

Free tier, no form to fill in. Signing in shares your email address with us — we store it to create your key and to recognise you if you sign in with another provider. See our Privacy Policy and Terms.

GitHub Google LinkedIn

A second provider on the same verified email joins the account you already have.