PDB Database Access
Note: This skill uses the RCSB PDB web API directly. No Modal deployment needed - all operations run locally via HTTP requests.
Fetching Structures
By PDB ID
# 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"
Using Python
from Bio.PDB import PDBList
pdbl = PDBList()
pdbl.retrieve_pdb_file("1ABC", pdir="structures/", file_format="pdb")
Using RCSB API
import requests
def fetch_pdb(pdb_id: str, format: str = "pdb") -> str:
"""Fetch structure from RCSB PDB."""
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:
"""Fetch sequence in FASTA format."""
url = f"https://www.rcsb.org/fasta/entry/{pdb_id}"
return requests.get(url).text
# Example usage
pdb_content = fetch_pdb("1ALU")
with open("1ALU.pdb", "w") as f:
f.write(pdb_content)
Structure Preparation
Selecting Chains
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
# Extract chain A
parser = PDBParser()
structure = parser.get_structure("protein", "1abc.pdb")
io = PDBIO()
io.set_structure(structure)
io.save("chain_A.pdb", ChainSelect("A"))
Trimming to Binding Region
def trim_around_residues(pdb_file, center_residues, buffer=10.0):
"""Trim structure to region around specified residues."""
parser = PDBParser()
structure = parser.get_structure("protein", pdb_file)
# Get center coordinates
center_coords = []
for res in structure.get_residues():
if res.id[1] in center_residues:
center_coords.extend([a.coord for a in res.get_atoms()])
center = np.mean(center_coords, axis=0)
# Keep residues within buffer
class RegionSelect(Select):
def accept_residue(self, res):
for atom in res.get_atoms():
if np.linalg.norm(atom.coord - center) < buffer:
return True
return False
io = PDBIO()
io.set_structure(structure)
io.save("trimmed.pdb", RegionSelect())
Searching PDB
RCSB Search API
import requests
query = {
"query": {
"type": "terminal",
"service": "full_text",
"parameters": {
"value": "EGFR kinase domain"
}
},
"return_type": "entry"
}
response = requests.post(
"https://search.rcsb.org/rcsbsearch/v2/query",
json=query
)
results = response.json()
By Sequence Similarity
query = {
"query": {
"type": "terminal",
"service": "sequence",
"parameters": {
"value": "MKTAYIAKQRQISFVK...",
"evalue_cutoff": 1e-10,
"identity_cutoff": 0.9
}
}
}
Structure Analysis
Get Chain Info
def get_structure_info(pdb_file):
parser = PDBParser(QUIET=True)
structure = parser.get_structure("protein", pdb_file)
info = {
"chains": [],
"total_residues": 0
}
for model in structure:
for chain in model:
residues = list(chain.get_residues())
info["chains"].append({
"id": chain.id,
"length": len(residues),
"first_res": residues[0].id[1],
"last_res": residues[-1].id[1]
})
info["total_residues"] += len(residues)
return info
Find Interface Residues
def find_interface_residues(pdb_file, chain_a, chain_b, distance=4.0):
"""Find residues at interface between two chains."""
parser = PDBParser(QUIET=True)
structure = parser.get_structure("complex", pdb_file)
interface_a = set()
interface_b = 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
Common Tasks for Binder Design
Target Preparation Checklist
- Download structure:
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"
- Identify target chain
- Remove waters and ligands (if needed)
- Trim to binding region + buffer
- Identify potential hotspots
- Renumber if needed
Troubleshooting
Structure not found: Check PDB ID format (4 characters)
Multiple models: Select first model for design
Missing residues: Check for gaps in structure
Next: Use structure with boltzgen (recommended) or rfdiffusion for design.
