Help me in understanding the PDB file

Question

Can anybody please explain the below line to me.

"We took the structure and coordinates of nogalamycin from the X-ray structure determined in PDB code = 1D17"

What do I need to download from there....a pdb file or what?

Thank you

Answer 1

well wasnt able to figure out how to make openapigenerator work with rcsb pdb ModelServer https://models.rcsb.org/, I ended up with this code copying the webserver manual input results for ligands:

import requests


def main():
   
  risposta = requests.get('https://models.rcsb.org/v1/1d17/ligand?encoding=cif&copy_all_categories=false&download=true&filename=out',
                          
                          allow_redirects=True)
  
  open('out.cif', 'wb').write(risposta.content)

  print(risposta.status_code)

if __name__ == '__main__':      
   
   main()

unfortunately the server gives you the wrong ligand (try it out)

it says :' ​/v1​/{id}​/ligand Coordinates of the first group satisfying the given criteria.'

tried with:

risposta = requests.get('https://models.rcsb.org/v1/1d17/ligand?label_atom_id=NGM&encoding=cif&copy_all_categories=false&download=true&filename=out',
                       
                       allow_redirects=True)

but no luck again, think problem is in downloaded file :

_model_server_params.name     atom_site 
_model_server_params.value    '{"label_atom_id":"NGM"}'  ###### here

but not an expert of APis and openAPI at all

EDITED:

eventually I got it right using in the code above:

risposta = requests.get('https://models.rcsb.org/v1/1d17/ligand?label_comp_id=NGM&encoding=cif&copy_all_categories=false&download=true&filename=out',
                      
                      allow_redirects=True) 

so I get a out.cif file containing NGM

using another database and FTP :

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 19 19:29:30 2021

@author: Pietro


https://bioinformatics.stackexchange.com/questions/18076/help-me-in-understanding-the-pdb-file#comment25289_18076

Ligand extract:
    
https://stackoverflow.com/questions/61390035/how-to-save-each-ligand-from-a-pdb-file-separately-with-bio-pdb

"""

from ftplib import FTP

import gzip

import os

from Bio.PDB import PDBParser, PDBIO, Select


def is_het(residue):
    res = residue.id[0]
    return res != " " and res != "W"


class ResidueSelect(Select):
    def __init__(self, chain, residue):
        self.chain = chain
        self.residue = residue

    def accept_chain(self, chain):
        return chain.id == self.chain.id

    def accept_residue(self, residue):
        """ Recognition of heteroatoms - Remove water molecules """
        return residue == self.residue and is_het(residue)


def extract_ligands(path):
    """ Extraction of the heteroatoms of .pdb files """

    for pfb_file in os.listdir(path):
        i = 1
        if pfb_file.endswith('.pdb') and not pfb_file.startswith("lig_"):
            pdb_code = pfb_file[:-4]
            pdb = PDBParser().get_structure(pdb_code, path + pfb_file)
            io = PDBIO()
            io.set_structure(pdb)
            for model in pdb:
                for chain in model:
                    for residue in chain:
                        if not is_het(residue):
                            continue
                        print(f"saving {chain} {residue}")
                        io.save(f"lig_{pdb_code}_{i}.pdb", ResidueSelect(chain, residue))
                        i += 1




def getFile(ftp, filename):
    try:
        # ftp.retrbinary("RETR", filename ,open(code+'.gz', 'wb').write)
        ftp.retrbinary("RETR " + filename ,open(code+'.gz', 'wb').write)
    except:
        print("Error somewhere !!!!")


code = '1D17'
filename = 'pdb'+code.lower()+'.ent.gz'                 ## pdb1D17.ent.gz    

print(filename)




ftp = FTP('ftp.wwpdb.org')   # connect to host, default port

# ftp.login()               # user anonymous, passwd anonymous@
print(ftp.login())

ftp.cwd('/pub/pdb/data/structures/all/pdb/')  

print(ftp.pwd()  )

getFile(ftp, filename)

zipped = gzip.open(code+'.gz', 'rb')

unzipped = zipped.read()

# print(unzipped)


saved = open(code+'.pdb', 'wb')

saved.write(unzipped)
saved.close()


path = './'

extract_ligands(path)

copying from : https://stackoverflow.com/questions/61390035/how-to-save-each-ligand-from-a-pdb-file-separately-with-bio-pdb

and using FTP from ftplib on http://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/ : PDB - FTP Archive over HTTP

NOGALAMYCIN is NGM third ligand downloaded (shuold be the only one according to https://www.rcsb.org/structure/1d17)

In any case I am failing at ubderstandung *,-) how https://models.rcsb.org/

Parameters are related to https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner%E2%80%99s-guide-to-pdb-structures-and-the-pdbx-mmcif-format , the mmcif format

but as I told before I can't read inside openapi.json OpenAPI Specification