science.pdb.structure

Get full details for a 3D protein structure by PDB ID — title, experimental method (X-ray/cryo-EM/NMR), resolution, molecular weight, chain counts (protein/DNA/RNA), deposit date, primary citation with DOI and PubMed ID. Essential for drug design and structural analysis (RCSB PDB)

SERVERApibase SOURCEapibase-mcp-client

Low RISK CLASS

Category Read

Parameters 11 required

Recommended Allowedsee the rule below

Registry record Grade F, identity unverified Pull the record →

This record as markdown: /tools/io-github-whiteknightonhorse-apibase/science.pdb.structure.md

WHAT IT DOES

What science.pdb.structure does on Apibase

AI agents call science.pdb.structure to retrieve information from Apibase without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.

Parameter	Type	Required	Description
`pdb_id`	string	Yes	4-character PDB identifier (e.g. "4HHB" for hemoglobin, "1BNA" for DNA, "6LU7" for SARS-CoV-2 main protease)

Parameters from the server's own tool schema.

RISK

Why science.pdb.structure is rated Low

Queries and retrieves public protein structure metadata from PDB database; no side effects.

From the tool's definition Get full details for a 3D protein structure by PDB ID — retrieves data only

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs science.pdb.structure safely

PolicyLayer is an MCP gateway: it sits between your AI agents and Apibase, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For science.pdb.structure, this is the rule to start with:

science.pdb.structure Allowed

science.pdb.structure is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "science.pdb.structure": {}
  }
}

ALLOW ONLY THIS TOOL → Instant setup, no code required.

The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every science.pdb.structure call is checked against it from then on.

FAQ

Questions about science.pdb.structure

What does the science.pdb.structure tool do? +

What parameters does science.pdb.structure accept? +

science.pdb.structure accepts 1 parameter: pdb_id. Required: pdb_id. The full parameter table on this page comes from the server's own tool schema.

How do I enforce a policy on science.pdb.structure? +

Register the Apibase MCP server in PolicyLayer and add a rule for science.pdb.structure: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Apibase. Nothing to install.

What risk level is science.pdb.structure? +

science.pdb.structure is a Read tool with low risk. Read-only tools are generally safe to allow by default.

Can I rate-limit science.pdb.structure? +

Yes. Add a rate_limit block to the science.pdb.structure rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block science.pdb.structure completely? +

Set action: deny in the PolicyLayer policy for science.pdb.structure. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides science.pdb.structure? +

science.pdb.structure is provided by the Apibase MCP server (apibase-mcp-client). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

KEEP EXPLORING

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