pdb

name: pdb description: > Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata.

For sequence lookup, use uniprot. For binder design workflow, use binder-design. license: MIT category: utilities tags: [database, structure, fetch] source: https://github.com/adaptyvbio/protein-design-skills

PDB Database Access

Note: Uses RCSB PDB web API directly. No Modal needed.

Fetching Structures

# Download PDB file
curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb"

# Download mmCIF
curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif"

import requests

def fetch_pdb(pdb_id: str, format: str = "pdb") -> str:
    url = f"https://files.rcsb.org/download/{pdb_id}.{format}"
    response = requests.get(url)
    response.raise_for_status()
    return response.text

def fetch_fasta(pdb_id: str) -> str:
    return requests.get(f"https://www.rcsb.org/fasta/entry/{pdb_id}").text

Structure Preparation

Extract chain

from Bio.PDB import PDBParser, PDBIO, Select

class ChainSelect(Select):
    def __init__(self, chain_id):
        self.chain_id = chain_id
    def accept_chain(self, chain):
        return chain.id == self.chain_id

parser = PDBParser()
structure = parser.get_structure("protein", "1abc.pdb")
io = PDBIO()
io.set_structure(structure)
io.save("chain_A.pdb", ChainSelect("A"))

Find interface residues

def find_interface_residues(pdb_file, chain_a, chain_b, distance=4.0):
    parser = PDBParser(QUIET=True)
    structure = parser.get_structure("complex", pdb_file)
    interface_a, interface_b = set(), set()
    for res_a in structure[0][chain_a].get_residues():
        for res_b in structure[0][chain_b].get_residues():
            for atom_a in res_a.get_atoms():
                for atom_b in res_b.get_atoms():
                    if atom_a - atom_b < distance:
                        interface_a.add(res_a.id[1])
                        interface_b.add(res_b.id[1])
    return interface_a, interface_b

RCSB Search API

import requests

query = {
    "query": {"type": "terminal", "service": "full_text",
              "parameters": {"value": "EGFR kinase domain"}},
    "return_type": "entry"
}
results = requests.post("https://search.rcsb.org/rcsbsearch/v2/query", json=query).json()

Target Preparation Checklist

1. Download structure: curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"
2. Identify target chain
3. Remove waters and ligands (if needed)
4. Trim to binding region + buffer
5. Identify potential hotspots

Next: Use structure with boltzgen or bindcraft for design.