I want to find the residues of human ACE 2 which interact with the spike protein of Covid-19?
or can anyone tell me a method to find the interaction residue for this PDB file?
PBD ID: 6lzg
thank you.
Be safe form covid-19
http://pic.mbu.iisc.ernet.in/
Harindu Rajapaksha
by downloading the protein and opening it with Biovia Discovery studio I checked the mentioned active site residues and here are they:
HIS374 HIS 378 GLU 402 OR (GLN340 GLU57 THR55 ASN53) OR (LYS26 ASN90) or (ASN322 MET323) or (PHE338 PHE342 PHE343).
you also can check the actual active site residues from Uniprot.
some researchers consider the native ligands that comes with the crystal structure position is the active site.
or you can use online servers for predicting it for you (which I don't prefer) such as:
http://www.pool.neu.edu/wPOOL/help.jsp
http://www.sbg.bio.ic.ac.uk/3dligandsite/ http://consurf.tau.ac.il/2016/
http://cssb.biology.gatech.edu/findsite
http://sts.bioe.uic.edu/castp/
http://www.scfbio-iitd.res.in/dock/ActiveSite.jsp
best regards
I am sending you a picture from Lan et al (2020) with all contact residues in ACE2 and Sars-Cov-2 interface.
Source: https://www.nature.com/articles/s41586-020-2180-5
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