structure
AI agents call structure to retrieve information from Mcp Rcsb Pdb without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
The 'structure' tool retrieves protein structure data from RCSB PDB without modifying or deleting data. It is a read-only query operation with no side effects. Low severity because misuse would only expose or retrieve existing scientific data, not cause harm or irreversible changes.
From the tool's definition Tool name 'structure' paired with server description stating it 'Enables querying and retrieving experimental protein structures' and sibling tools including 'search', 'summary', 'assembly', 'ligand', and 'polymer_entity' all indicating data retrieval…
Attacks that exploit this kind of access
structure. It is categorised as a Read tool in the Mcp Rcsb Pdb MCP Server, which means it retrieves data without modifying state.
Register the Mcp Rcsb Pdb MCP server in PolicyLayer and add a rule for 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 Mcp Rcsb Pdb. Nothing to install.
structure is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the 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.
Set action: deny in the PolicyLayer policy for 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.
structure is provided by the Mcp Rcsb Pdb MCP server (pipeworx-io/mcp-rcsb-pdb). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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