How to get the PDB id of a mystery sequence? - biopython

Question

I have a bunch of proteins, from something called proteinnet.
Now the sequences there have some sort of ID, but it is clearly not a PDB id, so I need to find that in some other way. For each protein I have the amino acid sequence. I'm using biopython, but I'm not very experienced in it yet and couldn't find this in the guide.
So my question is how do I find a proteins PDB id given that I have the amino acid sequence of the protein? (Such that I can download the PDB file for the protein)

Answer 1

hi I was playing a little bit ago with the RCSB PDB search API,
ended up with this piece of code (can't find examples on rcsb pdb website anymore),
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Dec 27 16:20:43 2020
#author: Pietro
"""
import PDB_searchAPI_5
from PDB_searchAPI_5.rest import ApiException
import json
#"value":"STEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"
# Defining the host is optional and defaults to https://search.rcsb.org/rcsbsearch/v1
# See configuration.py for a list of all supported configuration parameters.
configuration = PDB_searchAPI_5.Configuration(
host = "http://search.rcsb.org/rcsbsearch/v1"
)
data_entry_1 = '''{
"query": {
"type": "terminal",
"service": "sequence",
"parameters": {
"evalue_cutoff": 1,
"identity_cutoff": 0.9,
"target": "pdb_protein_sequence",
"value": "STEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"
}
},
"request_options": {
"scoring_strategy": "sequence"
},
"return_type": "entry"
}'''
# Enter a context with an instance of the API client
with PDB_searchAPI_5.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PDB_searchAPI_5.SearchServiceApi(api_client)
try:
# Get RCSB PDB data schema as JSON schema extended with RCSB metadata.
pippo = api_instance.run_json_queries_get(data_entry_1)
except ApiException as e:
print("Exception when calling SearchServiceApi->run_json_queries_get: %s\n" % e)
exit()
print(type(pippo))
print(dir(pippo))
pippox = pippo.__dict__
print('\n bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb \n' ,pippox)
print('\n\n ********************************* \n\n')
print(type(pippox))
pippoy = pippo.result_set
print(type(pippoy))
for i in pippoy:
print('\n',i,'\n', type(i))
print('\n LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL\n')
for i in pippoy:
for key in i:
print('\n', i['identifier'], ' score : ', i['score'])
the search module (import PDB_searchAPI_5) was generated with: openapi-generator-cli-4.3.1.jar link here
the open api specs where 1.7.3 now they are 1.7.15 see https://search.rcsb.org/openapi.json
the data_entry_1 bit was copied from rcsb pdb website but can't find it anymore,
it was saying something about mmseqs2 being the sofware doing the search, played with:
"evalue_cutoff": 1,
"identity_cutoff": 0.9,
parameters but didn't find a way to select only 100% identity
here the PDB_searchAPI_5 install it in a virtual enviroment with:
pip install PDB-searchAPI-5-1.0.0.tar.gz
was generated by openapi-generator-cli-4.3.1.jar with:
java -jar openapi-generator-cli-4.3.1.jar generate -g python -i pdb-search-api-openapi.json --additionalproperties=generateSourceCodeOnly=True,packageName=PDB_searchAPI_5
don't put spaces in --additionalproperties part (took one week to figure it out)
the README.md file is the most important part as it explain how to use the OPEN-API client
you need your fasta sequences here:
"value":"STEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"
the score = 1 should be the exact match,
probably the biopython blast module is easier, but it blast NIH database instead of RCSB PDB, sorry can't elaborate more on this, still need to figure out what is a JSON file, and wasnt able to find a better free tool that automatically generate a better OPEN-API python client (I believe is kind of not so easy task... but we always want more...)
to get API documentation try:
java -jar openapi-generator-cli-4.3.1.jar generate -g html -i https://search.rcsb.org/openapi.json --skip-validate-spec
You get html document or for pdf: https://mrin9.github.io/RapiPdf/
http://search.rcsb.org/openapi.json
works as well as https://search.rcsb.org/openapi.json so that you can look at the exchanges between client and server with wireshark