Is there a way to separate the chains belong to each Biological assembly in a PDB file?(python Script)

Question

I want to separate the chain IDs which belong to specific Biological assemblies in a PDB file. As an Example PDB ID 1BRS has 3 Biological assemblies Biological assembly 1 : - chains A and D Biological assembly 2 : - Chains B and E Biological assembly 3 : - chains C and F

Is there a way (python Script) to get the Chain IDs separate which belong to each biological assembly as follows 1BRS_A:D 1BRS_B:E 1BRS_C:F No need to extract the chain coordinates. If I get the chain names, that will be enough. Thanks in advance

Answer 1

The PDBx/mmCIF file format contains the information in the _pdbx_struct_assembly_gen category.

loop_
_pdbx_struct_assembly_gen.assembly_id 
_pdbx_struct_assembly_gen.oper_expression 
_pdbx_struct_assembly_gen.asym_id_list 
1 1 A,D,G,J 
2 1 B,E,H,K 
3 1 C,F,I,L 

These files can be read e.g. with Biotite (https://www.biotite-python.org/), a package I am developing. The categories can be read in a dictionary-like manner:

import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx

ID = "1BRS"

# Download structure
file_name = rcsb.fetch(ID, "pdbx", target_path=".")

# Read file
file = pdbx.PDBxFile()
file.read(file_name)
# Get 'pdbx_struct_assembly_gen' category as dictionary
assembly_dict = file["pdbx_struct_assembly_gen"]
for asym_id_list in assembly_dict["asym_id_list"]:
    chain_ids = asym_id_list.split(",")
    print(f"{ID}_{':'.join(chain_ids)}")

The output is

1BRS_A:D:G:J
1BRS_B:E:H:K
1BRS_C:F:I:L

The chains G-L contain only water molecules.

EDIT:

To include only chain IDs that belong to a polymer, e.g. a protein or a nucleotide, you can use the entity_poly category:

loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.nstd_linkage 
_entity_poly.nstd_monomer 
_entity_poly.pdbx_seq_one_letter_code 
_entity_poly.pdbx_seq_one_letter_code_can 
_entity_poly.pdbx_strand_id 
_entity_poly.pdbx_target_identifier 
1 'polypeptide(L)' no no 
;AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTS
GFRNSDRILYSSDWLIYKTTDHYQTFTKIR
;
;AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTS
GFRNSDRILYSSDWLIYKTTDHYQTFTKIR
;
A,B,C ? 
2 'polypeptide(L)' no no 
;KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAE
GADITIILS
;
;KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAE
GADITIILS
;
D,E,F ? 

This is the updated Python code:

import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx

ID = "1BRS"

# Download structure
file_name = rcsb.fetch(ID, "pdbx", target_path=".")

# Read file
file = pdbx.PDBxFile()
file.read(file_name)

# Get 'entity_poly' category as dictionary
# to find out which chains are polymers
poly_chains = []
for chain_list in file["entity_poly"]["pdbx_strand_id"]:
    poly_chains += chain_list.split(",")

# Get 'pdbx_struct_assembly_gen' category as dictionary
for asym_id_list in file["pdbx_struct_assembly_gen"]["asym_id_list"]:
    chain_ids = asym_id_list.split(",")
    # Filter chains that belong to a polymer
    chain_ids = [chain_id for chain_id in chain_ids if chain_id in poly_chains]
    print(f"{ID}_{':'.join(chain_ids)}")

And this is the output:

1BRS_A:D
1BRS_B:E
1BRS_C:F