mims-harvard/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")

Pick the structure that contains the right complex: include the binding partner chain you care about, the relevant ligand, and a resolution adequate for distance-based classification (≤ 3 Å is a safe default).

Step 2: Run the annotation

Structure_annotate_per_residue(
    pdb_id="6VJJ",
    target_chain="A",
    partner_chains=["B"],
    ligand_resnames=["GNP", "MG"],
    distance_cutoff=5.0,
    core_rsa_cutoff=0.25,
    include_secondary_structure=False,
)

Returns annotations: List[{position, aa, dist_partner, dist_ligand, rsa, region, is_core, ss_element?}] for every residue of the target chain. For KRAS in 6VJJ, this yields 168 rows.

Step 3: Verify the numbering before joining

PDB residue numbers carry silent offsets — crystal constructs add N-terminal cloning residues, and published figures sometimes shift the track relative to the panel sequence. Always verify with a landmark:

# Get the canonical reference sequence
UniProt_get_sequence_by_accession(accession="P01116")
# Then spot-check: KRAS canonical position 12 should be glycine
assert annotations[11]["aa"] == "G"  # 1-indexed position 12, 0-indexed index 11

If the landmark mismatches, record the offset explicitly (e.g. pdb_pos = uniprot_pos + offset) before any downstream join. Do not silently rebase positions.

Step 4: Combine with secondary structure (optional)

If you set include_secondary_structure=True, the tool fetches per-residue helix/strand/coil from PDBe REST. Alternatively, use the dedicated PDBe secondary-structure tool separately:

pdbe_get_entry_secondary_structure(pdb_id="6VJJ")
# Returns per-chain helix + strand ranges

Step 5: Use the annotation

The returned table is keyed by 1-based canonical residue number. Typical downstream uses:

| Use case | Field to read | |---|---| | Is variant X in a pocket? | by_pos = {a["position"]: a for a in annotations}; by_pos[X]["region"] in ("ligand", "both") — index by position field, NOT list index (PDB residue numbers may not start at 1 or be contiguous) | | Build a DMS heatmap annotation track | [(r["position"], r["region"], r["is_core"], r.get("ss_element"))] | | Filter SAE hotspot features to ligand-binding residues | filter clusters by region == "ligand" | | Compare buried vs surface signal | group statistics by is_core |

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Interpretation table

| Region label | Biological meaning | Common functional role | |---|---|---| | interface | Within distance_cutoff of a partner chain | Protein-protein binding residue; variants often disrupt complex formation | | ligand | Within distance_cutoff of a ligand heavy atom | Pocket residue; variants often disrupt substrate / cofactor / drug binding | | both | Both | Allosteric or shared-surface residue | | other | Neither | Surface (if not is_core) or core (if is_core) — variants impact through stability or distal effects | | is_core=true | RSA < core_rsa_cutoff (0.25 by default) | Buried residue; variants often destabilize the fold |

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Honest limitations

1. One conformer only. A static crystal structure does not capture alternative conformations or induced-fit binding. A residue may be at the pocket in one conformer and away in another. Pick the structure whose bound state matches your question.
2. Numbering is fragile. Crystal constructs add N-terminal tags or skip disordered N/C termini. Always verify with a landmark before joining to a sequence or to another annotation source. The skill cannot detect silent offsets for you.
3. Distance cutoff is a convention, not a truth. 5.0 Å is the literature default. Tighten to 4.0 Å for stricter pocket calls; loosen to 6.0 Å to include 2nd-shell residues.
4. freesasa RSA can exceed 1.0 for small / unusual structures because the max-ASA reference is calibrated for a typical protein context. For real well-folded proteins values cluster in [0, 1.2]; reading them as a fraction is fine, but treat extreme values as a flag to inspect.
5. partner_chains=[] is permitted but then all dist_partner values are null — interface analysis is skipped entirely.
6. HETATM ligands only. Modified residues (e.g. phosphoresidues already in the chain) are not detected as ligands — they are part of the chain.

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Cross-references

| Tool | Role | Use it for | |---|---|---| | Structure_annotate_per_residue | This skill's atomic tool | The annotation itself | | PDBeSIFTS_get_best_structures | UniProt → ranked PDB list | Step 1 | | PDBeSIFTS_get_all_structures | UniProt → full PDB list | Step 1 | | RCSBAdvSearch_search_structures | Free-text RCSB search | Step 1 | | UniProt_get_sequence_by_accession | Canonical sequence | Step 3 (numbering verification) | | pdbe_get_entry_secondary_structure | SS alone | Step 4 alternative | | tooluniverse-residue-functional-mechanism-interpretation | Downstream consumer | Use this annotation as the structural evidence layer when interpreting DMS hotspots; the skill also plots an annotated DMS heatmap in its Step 7 |