PDBe¶

Download and filter PDB files.

Download PDB files from PDBe¶

In [1]:

from pathlib import Path

from protein_quest.pdbe.fetch import fetch

from pathlib import Path from protein_quest.pdbe.fetch import fetch

In [2]:

ids = [
    "4NDY",  # structure of uniprot A8MT69
    "4DRA",  # structure of uniprot A8MT69
    "1XWH",  # structure of uniprot O43918
    "8WAS",  # structure for which there is no single pdb file
]

ids = [ "4NDY", # structure of uniprot A8MT69 "4DRA", # structure of uniprot A8MT69 "1XWH", # structure of uniprot O43918 "8WAS", # structure for which there is no single pdb file ]

In [3]:

save_dir = Path("pdb_files")

save_dir = Path("pdb_files")

In [5]:

files = await fetch(ids, save_dir)
files

files = await fetch(ids, save_dir) files

Downloading PDBe mmCIF files: 100%|██████████| 4/4 [00:00<00:00,  7.85it/s]

Out[5]:

{'4NDY': PosixPath('pdb_files/4ndy.cif.gz'),
 '4DRA': PosixPath('pdb_files/4dra.cif.gz'),
 '1XWH': PosixPath('pdb_files/1xwh.cif.gz'),
 '8WAS': PosixPath('pdb_files/8was.cif.gz')}

In [6]:

!ls pdb_files

!ls pdb_files

1xwh.cif.gz  4dra.cif.gz  4ndy.cif.gz  8was.cif.gz

Prepare pdb file for haddock3 or powerfit¶

Haddock3 and powerfit like to have a file with a single protein in it called chain "A". The protein-quest package can help to create such a file.

In [7]:

from protein_quest.pdbe.io import write_single_chain_pdb_file

from protein_quest.pdbe.io import write_single_chain_pdb_file

In [ ]:

# A8MT69	4NDY	B/D/H/L/M/N/U/V/W/X=8-81
# above is the identifier, chain and position info for the structure from https://www.uniprot.org/uniprotkb/A8MT69/entry#structure
output_4dny_file = write_single_chain_pdb_file(input_file=save_dir / "4ndy.cif.gz", chain2keep="B", output_dir=save_dir)
output_4dny_file

# A8MT69 4NDY B/D/H/L/M/N/U/V/W/X=8-81 # above is the identifier, chain and position info for the structure from https://www.uniprot.org/uniprotkb/A8MT69/entry#structure output_4dny_file = write_single_chain_pdb_file(input_file=save_dir / "4ndy.cif.gz", chain2keep="B", output_dir=save_dir) output_4dny_file

Out[ ]:

PosixPath('pdb_files/4ndy_B2A.cif.gz')

In [ ]:

# A8MT69	4DRA	E/F/G/H=1-81
output_4dra_file = write_single_chain_pdb_file(input_file=save_dir / "4dra.cif.gz", chain2keep="E", output_dir=save_dir)
output_4dra_file

# A8MT69 4DRA E/F/G/H=1-81 output_4dra_file = write_single_chain_pdb_file(input_file=save_dir / "4dra.cif.gz", chain2keep="E", output_dir=save_dir) output_4dra_file

Out[ ]:

PosixPath('pdb_files/4dra_E2A.cif.gz')

In [12]:

output_1xwh_file = write_single_chain_pdb_file(
    input_file=save_dir / "1xwh.cif.gz",
    chain2keep="A",
    output_dir=save_dir,
)
output_1xwh_file

output_1xwh_file = write_single_chain_pdb_file( input_file=save_dir / "1xwh.cif.gz", chain2keep="A", output_dir=save_dir, ) output_1xwh_file

Out[12]:

PosixPath('pdb_files/1xwh_A2A.cif.gz')

In [14]:

# O00268      │ 8WAS    │ D/d=1-1085
output_8was_file = write_single_chain_pdb_file(
    input_file=save_dir / "8was.cif.gz",
    chain2keep="D",
    output_dir=save_dir,
)
output_8was_file

# O00268 │ 8WAS │ D/d=1-1085 output_8was_file = write_single_chain_pdb_file( input_file=save_dir / "8was.cif.gz", chain2keep="D", output_dir=save_dir, ) output_8was_file

Out[14]:

PosixPath('pdb_files/8was_D2A.cif.gz')

In [17]:

!ls -sh -1 pdb_files/

!ls -sh -1 pdb_files/

total 4.1M
 16K 1xwh_A2A.cif.gz
380K 1xwh.cif.gz
276K 4dra.cif.gz
 24K 4dra_E2A.cif.gz
 28K 4ndy_B2A.cif.gz
832K 4ndy.cif.gz
2.6M 8was.cif.gz
 24K 8was_D2A.cif.gz

In [ ]: