Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.
Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.
license
MIT
allowed-tools
Read Write Edit Bash
compatibility
Requires Python 3.10+ and outbound HTTPS access to rest.uniprot.org, search.rcsb.org, data.rcsb.org, files.rcsb.org, and alphafold.ebi.ac.uk. The bundled scripts use only the Python standard library and need no API key or account.
The retrieval layer under every structure-based workflow: sequence in, annotation and
coordinates out, plus the checks that decide whether those coordinates are worth using.
What is this protein, what is its sequence, where are its sites, what ids does it map to
rcsb_search.py
Which structures exist, and which are worth downloading
fetch_structure.py
Get the coordinates — experimental, assembly, predicted, or ligand
structure_report.py
Is this file actually usable, and what is missing from it
Sequence and annotation
python skills/uniprot-rcsb/scripts/uniprot_fetch.py entry P00533
python skills/uniprot-rcsb/scripts/uniprot_fetch.py search "gene:EGFR AND organism_id:9606 AND reviewed:true"
python skills/uniprot-rcsb/scripts/uniprot_fetch.py fasta P00533 --isoforms
python skills/uniprot-rcsb/scripts/uniprot_fetch.py features P00533 --types Binding,Active,Mutagenesis
python skills/uniprot-rcsb/scripts/uniprot_fetch.py map P00533 P04637 --to PDB
Put reviewed:true in almost every search. UniProtKB is ~0.5 % Swiss-Prot (curated) and
~99.5 % TrEMBL (automatic); without the flag a gene-name search returns fragments and predicted
isoforms above the entry you wanted. The script reports the reviewed/unreviewed split and warns
when nothing reviewed matched.
Two UniProt behaviours the script absorbs: pagination lives in the HTTP Link header, not the
JSON body — read only the body and you silently get the first page of many — and gzip-encoded
responses are sometimes , so one decompression leaves bytes that fail much
later as a on byte 1.
doubly wrapped
UnicodeDecodeError
Finding structures
# what does UniProt already cross-reference, with the residue range each covers?
python skills/uniprot-rcsb/scripts/uniprot_fetch.py pdb P00533 --max-resolution 2.0
# search the PDB properly, with ligands and mutations resolved
python skills/uniprot-rcsb/scripts/rcsb_search.py uniprot P00533 \
--max-resolution 2.0 --has-ligand --exclude-mutants
python skills/uniprot-rcsb/scripts/rcsb_search.py sequence --fasta target.fasta --identity 0.9
python skills/uniprot-rcsb/scripts/rcsb_search.py ligand STI
python skills/uniprot-rcsb/scripts/rcsb_search.py text "SARS-CoV-2 main protease" --max-resolution 1.5
The RCSB search API returns only identifiers and scores — no resolution, no ligands, no
method. Every useful question therefore needs a second service, and the script batches that
through the data GraphQL endpoint (one request for 25 hits instead of ~60 REST calls).
Two traps it handles: a search with no hits answers HTTP 204 with an empty body, which
json.loads turns into a parse error rather than "nothing matched"; and the default
results_content_typeincludes computational models, so an unqualified search quietly mixes
AlphaFold predictions into a list that looks like crystal structures. The script pins
experimental.
--has-ligand excludes waters, ions, and crystallisation additives (SO4, GOL, EDO, PEG,
MPD, …). Without that exclusion, essentially every crystal structure looks holo.
Default to mmCIF. Legacy .pdb does not exist for entries that overflow the 80-column format
— large complexes and most recent cryo-EM structures — and files.rcsb.org/download/8ETU.pdb is
a 404. The script says so explicitly rather than passing the 404 through.
The asymmetric unit is not the biological unit. Deposited coordinates may hold half a dimer
or four copies of a monomer. Use assembly when an interface matters.
AlphaFold output reports the confidence bands before you commit:
# AF-P00533-F1 (Epidermal growth factor receptor) mean pLDDT: 75.94
band percent
very high (>90) 47.4
confident (70-90) 23.3
low (50-70) 6.5
very low (<50) 22.8
An excellent kinase domain attached to a disordered tail that is 23 % of the model. Trim to the
confident region; a full-length model in a simulation box spends most of its atoms on a
prediction nobody makes. And note that PAE, not pLDDT, governs domain arrangement — two
confident domains can still have a guessed relative orientation.
## ISSUES
- 24 residues unresolved inside the modelled range (A:734-737,748-754,868-874,1004-1009)
- 10 residues present in the construct but not modelled at the chain termini (A:696-700,1018-1022)
- no hydrogens (normal for X-ray) -- add them at your target pH during receptor preparation
- 126 water atoms present -- decide deliberately which to keep
- chain A: residues of interest are UNRESOLVED: [750]
That last line is the point. 3POZ is a 1.5 Å structure, and a residue in the region you asked
about has no coordinates at all — your pocket has a hole in one wall, and every docking score
computed against it is optimistic. Resolution does not tell you this; nothing tells you this
except looking.
The report reads PDB and mmCIF with no parser dependency, and covers chains and numbering gaps,
non-polymer ligands with occupancy, waters and additives, alternate conformations, insertion
codes, multiple models, and hydrogens. It reads unresolved residues from REMARK 465 /
_pdbx_unobs_or_zero_occ_residues, which is the only way to see terminal truncation — those
leave no gap in the numbering, so a report built from coordinates alone calls a truncated
construct complete.
Numbering will not line up
UniProt numbers the canonical isoform from 1. A PDB entry carries both auth_seq_id (the
depositor's numbering) and label_seq_id (a 1-based construct index), and expression tags and
deletions shift both. Map explicitly — via rcsb_polymer_entity_align, or by aligning
structure_report.py --sequence output against the UniProt sequence. Never assume residue 790 in
the paper is residue 790 in the file.
Composing with the rest of the bundle
open-targets → this skill: its proteinIds are the UniProt accessions to start from.
This skill → autodock-vina: a checked receptor plus a reference ligand for the box.
This skill → boltz: sequences for cofolding when no suitable structure exists.
This skill → molecular-dynamics / diffdock: coordinates, with the gaps known in advance.
This skill → esm / antibody-engineering: sequences for language models and numbering.
chembl uses UniProt accessions as its target key, so target_components__accession=P00533
joins the two directly.
Reporting honestly
Name the PDB id and its resolution, or the AlphaFold model version and its pLDDT distribution.
Say whether you used the asymmetric unit or an assembly. Say which residues near the site of
interest were unresolved. A structure-based result whose provenance is "the EGFR structure" is
not reproducible.
