Problems about the pKa prediction of two close ASP residues

[qingwang666]

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.
   

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!
   

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

[sobolevnrm]

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 <[email protected]> Sent: Monday, July 6, 2020 7:50 AM To: jensengroup/propka <[email protected]> Cc: Subscribed <[email protected]> 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? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjensengroup%2Fpropka%2Fissues%2F81&data=02%7C01%7C%7C80232b07d3774fa64d3808d821bbe8f8%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637296438226603331&sdata=xyUhWLEaVsmt81uJc3ilPy0TppKFB504NKWtaP%2FU3d0%3D&reserved=0>, or unsubscribe<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAOX7WGSQ4LD4T2FP45BO73R2HQCXANCNFSM4ORV2HVA&data=02%7C01%7C%7C80232b07d3774fa64d3808d821bbe8f8%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637296438226603331&sdata=rib01AJeqA6UDS6b1RnPeUI3Rk3XKOtvPuo9Ar10T1U%3D&reserved=0>.