SMTL ID : 8cac.1

Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x O6K: ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate(Covalent)

O6K.1: 18 residues within 4Å: Chain A: T.26, H.41, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, Y.172, D.187, R.188, Q.189 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.142, A:M.165, A:E.166, A:D.187, A:Q.189 Hydrogen bonds: A:F.140, A:G.143, A:S.144, A:C.145, A:H.164, A:E.166, A:E.166, A:E.166 O6K.2: 18 residues within 4Å: Chain B: T.26, H.41, M.49, F.140, L.141, N.142, G.143, S.144, C.145, H.163, H.164, M.165, E.166, L.167, P.168, Y.172, D.187, R.188 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.142, B:M.165, B:E.166 Hydrogen bonds: B:G.143, B:S.144, B:S.144, B:C.145, B:H.164, B:E.166, B:E.166, B:E.166 Water bridges: B:H.41

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain B: S.284, A.285, L.286 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ibrahim, M. et al., Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K. To Be Published

Release Date

2024-08-07

Peptides

3C-like proteinase nsp5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

3C-like proteinase nsp5