Primary sequence of PDB id

Question

[Bioinformatics313]

I understand that every protein accession may have one or multiple PDB id, and I know each PDB id also can have one or multiple chains. I do not understand where I find the primary sequence of each PDB id which has the same sequence as protein sequence in accession. Please anyone can explain or clarify that to me. I really appreciate any help. Thanks

[Joe]

What are you calling the primary sequence?

If a PDB ID has multiple chains, do you want all of them?

[Bioinformatics313]

I mean the primary structure of the protein. Does the PDB ID has the same primary structure as the accession? Thanks for reply

[Ram]

"Primary structure" is a term for sequence, if I remember my lessons from undergrad correctly. Is that what you mean? Are you asking if the sequence of the protein as found in the PDB entry is the same as the sequence of the protein as found in, say, UniProtKB-SwissProt?

[Bioinformatics313]

Thanks, RamRS for your reply. Yes, I meant exactly what you have mentioned in your question! How can I find the primary structure in PDB entry that matches with protein accession sequence?

[Ram]

You should be able to use the DBREF flag to get to the corresponding UniProt entries. For example, the DBREF entry for 3HG2 (in PDB format)looks like this:

DBREF  3HG2 A   32   429  UNP    P06280   AGAL_HUMAN      32    429             
DBREF  3HG2 B   32   429  UNP    P06280   AGAL_HUMAN      32    429

Both chains point to P06280, which I know is the canonical entry for Human GLA. There's also the SEQRES section if you're interested in the exact sequence in the PDB entry.

Here's an example (1A3N, human hemoglobin) where the PDB entry has links to multiple UniProt entries:

DBREF  1A3N A    1   141  UNP    P69905   HBA_HUMAN        1    141             
DBREF  1A3N B    1   146  UNP    P68871   HBB_HUMAN        1    146             
DBREF  1A3N C    1   141  UNP    P69905   HBA_HUMAN        1    141             
DBREF  1A3N D    1   146  UNP    P68871   HBB_HUMAN        1    146

[Bioinformatics313]

Thank you so much for your reply. I really appreciate it. But please I know how I get the PDB code for the protein accession. I meant how I GET THE sequence of the PDB id that match with the sequence in the accession. For example: This is the fast file for YP_009208550.1 accession

>YP_009208550.1 terminase large subunit [Mycobacterium phage Kikipoo]
MSYPDEPLSPIIEIPSPDAPDPDVWGEDGAYDERKAAVILEQAKSWSTEQKHAMLASLRAAKARASMKVK
YAHPAELAAALDPNYVVTPAIELISTSIERVLTSPKQINLEISMPPQEGKSTLAAVATPLRALQHNPHRK
IILATYALDLAETHSRTMREWIETYGTDVVDPLTGLPVEDKIGLKLARGANKVTAWSVAGGRGGLVAAGI
GSRLTGMPADLMIIDDPFKNMMEADSALYRKRVDEWFSSVARTRLAPDASIIMIQTRWHPEDLAGKVIAA
ERSLPRNERTWRVINIPAIAEKGIPDALKREPGTPMVSARDTPEAKRNFPKIRREVGERTWYALYQGSPR
NPEGGIFQQKWFDATRLPEAPLNPYTAVVGIDPADSGEGDEAGIIGGMAATIDKRLTAVLTHDRSGQYTS
DQWAKVGVTLALEIGARVLAVEGYTTAKTYTRVVREAYNAIHREARKKQLAGVPLTPVEHRALPDLPPFT
IKPWRGANKADAVARAGGMSQSFETGRARTIDYALATFEQQAVDWQAGQHQPDRVAAGIIVHDTIFDLMG
GTMSIAAPPTGSNPSGGQGREIPPPPAWMRRSIGK

suppose it has multiple PDB ids . How I can find the corresponding primary structure sequence for these ids

[Ram]

You need to explain what you mean by the following terms, as your usage of them is pretty ambiguous:

• PDB code (what's "code"?)
• protein accession (accession is like saying "ID". Which database are you talking about?)
• PDB id (Is this the PDB alphanumeric identifier? What's "code" then?)

Lastly, are you looking to go from a sequence input to a structure result? Are you blast-ing protein sequences against PDB and looking to pick the exact match results?

[Joe]

If it has multiple PDB IDs, they are all equivalent, so that sequence is THE sequence. There is nothing else to do.