How can I remove ligands in PDB structure?
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3 months ago
jsw940 ▴ 10

Hello,

I have a question about comparing the structures of two proteins.

I tried to compare two proteins using superposing in expasy but there is a problem.

As you see, a structure from the official PDB file has RNA parts interacting with protein.

I just want to compare protein versus protein. Then, how can I remove that nucleotide parts?

Thanks!

strcture

PDB structure protein • 235 views
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Open PDB file in a text editor, and remove RNA coordinates.As I understand, protein viewers such as SPDBV allows you to hide the element of your choice. Check if the software you are using, allows you to hide intercalating RNA.

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Thank you very much! I made images that I want using SPDBV. It really helps me.

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3 months ago
jgreener ▴ 380

If it's just one case, manually delete the ATOM/HETATM records you don't need from the PDB file.

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Thank you! I could edit my PDB files using MS excel. And that RNA parts really removed!

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