RCSB PDB · Agentic Access

RCSB PDB Agentic Access

x-agentic-access generated

RCSB PDB exposes 28 API operations that an AI agent could call, of which 10 are state-changing ‘acting’ operations. This is a recommended x-agentic-access execution contract — the scope, audience, consequence tier, short-lived token constraints, and escalation each action should carry before it is handed to an autonomous agent.

By consequence: 18 read and 10 write.

Contracts are classified heuristically from the provider’s OpenAPI and refresh on every APIs.io network build; audience is bound per deployment. The model follows Curity’s Access Intelligence (apidays Munich 2026). Browse every provider’s agent contracts at agentic-access.apis.io.

Structural BiologyProteomicsBioinformaticsGenomicsLife SciencesOpen DataResearchMacromoleculesCrystallographyNMR
Operations: 28 Acting: 10 Human-in-the-loop: 0 Method: generated

By consequence

read 18 write 10

Source

Agentic Access

Raw ↑ 
generated: '2026-07-15'
method: generated
source: openapi/rcsb-pdb-model-server-api.json, openapi/rcsb-pdb-search-api.json, openapi/rcsb-pdb-volume-server-api.json
description: Recommended x-agentic-access execution contracts, classified heuristically from
  the OpenAPI. A governance starting point for exposing this API to AI agents — review and bind
  audience per deployment. See research/curity/agentic-governance/.
summary:
  operations: 28
  by_action_class:
    connected: 18
    acting: 10
  by_consequence:
    read: 18
    write: 10
  human_in_the_loop_required: 0
operations:
- path: /v1/{id}/assembly
  method: get
  operationId: assembly
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/assembly
  method: post
  operationId: assembly-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/atoms
  method: get
  operationId: atoms
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/atoms
  method: post
  operationId: atoms-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/full
  method: get
  operationId: full
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/full
  method: post
  operationId: full-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/ligand
  method: get
  operationId: ligand
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/ligand
  method: post
  operationId: ligand-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/residueInteraction
  method: get
  operationId: residueInteraction
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/residueInteraction
  method: post
  operationId: residueInteraction-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/residueSurroundings
  method: get
  operationId: residueSurroundings
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/residueSurroundings
  method: post
  operationId: residueSurroundings-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/surroundingLigands
  method: get
  operationId: surroundingLigands
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/surroundingLigands
  method: post
  operationId: surroundingLigands-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/{id}/symmetryMates
  method: get
  operationId: symmetryMates
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/{id}/symmetryMates
  method: post
  operationId: symmetryMates-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /v1/query-many
  method: get
  operationId: query-many
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /v1/query-many
  method: post
  operationId: query-many-post
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /rcsbsearch/v2/query
  method: get
  operationId: runJsonQueriesGet
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /rcsbsearch/v2/query
  method: post
  operationId: runJsonQueriesPost
  x-agentic-access:
    action-class: acting
    consequence: write
    subject: required
    audience: null
    token:
      max-ttl: 900
    escalation:
      human-in-the-loop: conditional
      triggers:
      - abnormal
      - high-value
    audit: required
- path: /rcsbsearch/v2/suggest
  method: get
  operationId: getSuggestions
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /rcsbsearch/v2/query/unreleased
  method: get
  operationId: runUnreleasedEntryJsonQueries
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /rcsbsearch/v2/metadata/unreleased/schema
  method: get
  operationId: getUnreleasedEntryMetadata
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /rcsbsearch/v2/metadata/schema
  method: get
  operationId: getMetadata
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /rcsbsearch/v2/metadata/chemical/schema
  method: get
  operationId: getChemicalMetadata
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /{source}/{id}/
  method: get
  operationId: getInfo
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /{source}/{id}/box/{a1,a2,a3}/{b1,b2,b3}/
  method: get
  operationId: getBox
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none
- path: /{source}/{id}/cell/
  method: get
  operationId: getCell
  x-agentic-access:
    action-class: connected
    consequence: read
    subject: optional
    token:
      max-ttl: 3600
    audit: none