Aminoacids range of protein domains in PDB structures

Question

[Jimpix]

Hi!

It is available in to download information about amino acids range of protein domains from each PDB structure from some database?

Thanks for any answers!

EDIT: I mean position of the domains in the PDB structure, for example in 1PSR it would be from 12aa - 44aa and 50 aa - 85 aa. I want the file with information about domains positions. Or merge domains architectures from https://www.ebi.ac.uk/interpro/entry/pfam/PF00397/domain_architecture/ with ID PDB structures. It is possible?

Thanks in advance!

[Ram]

This post has an answer, it does not make sense to delete it when you just wanted to add additional information. I've copied over the additional information from your other post and deleted that one.

Answer 1

[Mensur Dlakic]

What does amino acids range mean? Length range? Frequency range?

Sequences of all proteins in PDB are available from:

https://files.wwpdb.org/pub/pdb/derived_data/

Look for the file pdb_seqres.txt. Whatever it is exactly that you need, it is likely to be in that file.

[Jimpix]

I mean position of the domains in the PDB sctructure, for example in 1PSR it would be from 12aa - 44aa and 50 aa - 85 aa. I want the file with information about domains positions. Or merge domains architectures from https://www.ebi.ac.uk/interpro/entry/pfam/PF00397/domain_architecture/ with ID PDB structures. It is posible? Mensur Dlakic

Answer 2

[Jiyao Wang]

You could try iCn3D to retrieve 3D domain or conserved domain range information for PDB or AlphaFold structures. One example is at https://structure.ncbi.nlm.nih.gov/icn3d/share.html?bPSkpeshtiH1TxbP8.

You can programmatically retrieve the domain ranges using the Node.js script https://github.com/ncbi/icn3d/blob/master/icn3dnode/annotation.js. One example command is "node annotation.js A0A044R7Z7 5", where 5 is for 3D domains.