tooluniverse-protein-structural-annotation-pdb

Protein structural annotation from a PDB

For each residue of a target protein chain, classify whether it sits at a binding interface, in a ligand pocket, is buried vs solvent-exposed, and (optionally) which secondary-structure element it belongs to. This is the annotation track that anchors any DMS heatmap or per-residue interpretation to the protein's actual physical context.

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When to use this skill

• Building a per-residue annotation track for a DMS heatmap
• Deciding whether a variant of interest is in an interface, in a pocket, or in the core — context that often distinguishes plausible mechanisms
• Reading SAE feature drops at a position against the protein's known biology (a feature drop at a ligand-pocket residue means something different from a drop at a surface residue)

Not for:

• Multi-conformer ensembles or NMR structure comparisons → use tooluniverse-computational-biophysics
• Whole-structure pocket detection without a known ligand → use a docking tool (e.g. SwissDock) or PDBe's pre-computed pockets

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Required inputs

Input	Format	Example
PDB ID	4 characters	6VJJ (KRAS-RAF1-GTP analogue)
Target chain	single character	A
Partner chain(s)	list of chain IDs	["B"]
Ligand resnames	3-letter PDB names	["GNP", "MG"]

Optional:

• distance_cutoff (default 5.0 Å)
• core_rsa_cutoff (default 0.25)
• include_secondary_structure (default false; uses PDBe REST if true)
• pdb_content instead of pdb_id for local / predicted structures

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Workflow

Step 1 (optional): Find the relevant PDB

If you only have a UniProt accession or gene symbol, pick a structure first:

# PDBe's curated UniProt→PDB mapping (recommended; ranks by coverage + resolution)
PDBeSIFTS_get_best_structures(uniprot_accession="P01116")
# Returns a ranked list of PDB IDs for KRAS with chain mapping

# Or full list (unranked)
PDBeSIFTS_get_all_structures(uniprot_accession="P01116")

# RCSB advanced search (free-text, when you don't have a UniProt yet)
RCSBAdvSearch_search_structures(query="KRAS GTP complex")