How to extract subset of protein structure (PDB format) file based on a subsequence of protein

[Edward Wijaya]

I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website.
The corresponding fasta sequence for that structure is this:

>2LY4_1|Chain A|High mobility group protein B1|Homo sapiens (9606)
GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGE
>2LY4_2|Chain B|Cellular tumor antigen p53|Homo sapiens (9606)
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPL

And the PDB format file can be downloaded here (1.7MB). The entire is to large to be pasted here.

What I want to do is to extract the subset of PDB format based on the subsequence in fasta above.
Namely Chain A starting from 1st residue to 30th residue

GKGDPKKPRGKMSSYAFFVQTCREEHKKKH

How can I do that with Bio3D?

[Xinqiu Yao]

If you know the residue numbers of the matched sequence, it would be easy to do with the atom.select() funciton.

For example, to create a subset containing residues 20-80:

spdb ← atom.select(pdb, resno=c(20:80), value=TRUE)

[Edward Wijaya]

Thanks. This works.