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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Problems about the pKa prediction of two close ASP residues #81

Open qingwang666 opened 4 years ago

qingwang666 commented 4 years ago

I use propka3.0 to predict the protonation state of one structure (PDBID: 2g1n).

  1. When only considering the receptor (i.e. without the ligand), the result is ASP33, ASH221. But the added proton of ASH221 seems to be weird because the best state will be the proton shared with the other ASP residue.
    image2

  2. When considering the ligand, the result is ASH33, ASP221. The added proton could share with the other ASP residue. But the distance between the added proton and the proton of amino is only 1.208 angstroms! image1

Something maybe wrong. Could you please give me some advice?

sobolevnrm commented 4 years ago

Hello --

Can you please say more about the software you used to the add the protons? Was it through PDB2PQR using PROPKA or some other mechanism?

Thank you.

From: QingWANG notifications@github.com Sent: Monday, July 6, 2020 7:50 AM To: jensengroup/propka propka@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [jensengroup/propka] Problems about the pKa prediction of two close ASP residues (#81)

I use propka3.0 to predict the protonation state of one structure (PDBID: 2g1n).

  1. When only considering the receptor (i.e. without the ligand), the result is ASP33, ASH221. But the added proton of ASH221 seems to be weird because the best state will be the proton shared with the other ASP residue. [image2]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F30262572%2F86604833-78474800-bfd8-11ea-9cea-cfbabe4a7a2f.png&data=02%7C01%7C%7C80232b07d3774fa64d3808d821bbe8f8%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637296438226593337&sdata=SZE78QqQBwBNEUjArEtlNvsV5zNpatFFGJfT50lJCSo%3D&reserved=0

  2. When considering the ligand, the result is ASH33, ASP221. The added proton could share with the other ASP residue. But the distance between the added proton and the proton of amino is only 1.208 angstroms! [image1]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F30262572%2F86604831-77161b00-bfd8-11ea-8250-aa19eee477ee.png&data=02%7C01%7C%7C80232b07d3774fa64d3808d821bbe8f8%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637296438226593337&sdata=W6vQYKBOAruUsw4Pv2xJC1jDO%2BySLdzsUkbBybX3wjY%3D&reserved=0

Something maybe wrong. Could you please give me some advice?

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