pdb-entry

Fetch 3D macromolecular structure metadata from RCSB PDB by entry ID.

SERVERMeta Data Mcp SOURCEpypi:meta-data-mcp

Low RISK CLASS

Category Read

Parameters 00 required

Recommended Allowedsee the rule below

Registry record Grade F, identity unverified Pull the record →

This record as markdown: /tools/io-github-derekslinz-meta-data-mcp/pdb-entry.md

WHAT IT DOES

What pdb-entry does on Meta Data Mcp

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

RISK

Why pdb-entry is rated Low

This tool queries a public scientific database (RCSB PDB — Protein Data Bank) to retrieve existing structural metadata. There is no data creation, modification, deletion, code execution, or financial impact. The operation is a simple GET request against an open API. Even if misused, an AI agent can only retrieve data that is already publicly available, posing minimal risk.

From the tool's definition Tool name 'pdb-entry' and description 'Fetch 3D macromolecular structure metadata from RCSB PDB by entry ID' indicate a retrieval operation.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs pdb-entry safely

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

pdb-entry Allowed

pdb-entry 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": {
    "pdb-entry": {}
  }
}

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

The button opens the PolicyLayer dashboard: create your workspace, connect Meta Data Mcp, apply this rule, and every pdb-entry call is checked against it from then on.

FAQ

Questions about pdb-entry

What does the pdb-entry tool do? +

Fetch 3D macromolecular structure metadata from RCSB PDB by entry ID. It is categorised as a Read tool in the Meta Data Mcp MCP Server, which means it retrieves data without modifying state.

How do I enforce a policy on pdb-entry? +

Register the Meta Data MCP server in PolicyLayer and add a rule for pdb-entry: 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 Meta Data Mcp. Nothing to install.

What risk level is pdb-entry? +

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

Can I rate-limit pdb-entry? +

Yes. Add a rate_limit block to the pdb-entry 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 pdb-entry completely? +

Set action: deny in the PolicyLayer policy for pdb-entry. 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 pdb-entry? +

pdb-entry is provided by the Meta Data MCP server (pypi:meta-data-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

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