Download fasta file for pdb id from uniprot

[bio_informatics]

Hi Members,
I've a list of pdb id [some ~80].
I want to download their fasta file from Uniprot.

I have been unable to find URL which can be then utilized using wget or curl.

example: 2rh1
Please help.

[GenoMax]

If you have 80 perhaps getting the fasta files for UniProt/SwissProt and UniProt/TreEmbl (ftp://ftp.uniprot.org/pub/databases/...base/complete/) then parsing out the sequences you need.

[bio_informatics]

Thank you GenoM for your reply.

I downloaded sprot [swissprot] file. On going through it, I found protein name as:

>sp|Q6GZX3|002L_FRG3G Uncharacterized protein 002L OS=Frog virus 3 (isolate Goorha) GN=FV3-002L PE=4 SV=1

I have pdb ids with me, and not much information other than that.
I was wondering how would I be able to get hold my data from this header.

Appreciate your inputs.

If you have 80 perhaps getting the fasta files for UniProt/SwissProt and UniProt/TreEmbl (ftp://ftp.uniprot.org/pub/databases/...base/complete/) then parsing out the sequences you need.

[bio_informatics]

I guess 6GZX are the PDB ids. I am randomly grep-ping the ids and have hit few of them.
But there are multiple entries for one such id.

$ grep -i "2m3g" uniprot_sprot.fasta

>sp|Q2M3G0|ABCB5_HUMAN ATP-binding cassette sub-family B member 5 OS=Homo sapiens GN=ABCB5 PE=1 SV=3

>sp|Q2M3G4|SHRM1_HUMAN Protein Shroom1 OS=Homo sapiens GN=SHROOM1 PE=1 SV=1

[GenoMax]

PDB to Uniprot ID's: http://www.uniprot.org/docs/pdbtosp

[bio_informatics]

Wow. That helps a lot. Thank you.

FASTA sequence/file can be downloaded using wget from a URL:

Ex:
pdb id -2E9Q

wget "http://www.uniprot.org/uniprot/?query=database%3A%28type%3Apdb+2E9Q%29&format=fasta"

Note: There can be multiple sequences of one PDB id.

http://www.uniprot.org/uniprot/?query=database%3A%28type%3Apdb+AND+15C8%29+&format=fasta