SMTL ID : 8e7n.1

Crystal structure of beluga whale Gammacoronavirus SW1 Mpro with GC-376 captured in two conformational states

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x K36: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)

K36.1: 17 residues within 4Å: Chain A: H.41, K.45, F.137, M.138, S.139, G.140, S.141, C.142, H.160, H.161, L.162, E.163, H.169, D.184, E.186 Ligands: B1S.2, GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, A:K.45, A:D.184, A:E.186 Hydrogen bonds: A:G.140, A:S.141, A:C.142, A:H.161, A:E.163, A:E.163, A:E.186 K36.5: 20 residues within 4Å: Chain A: A.1 Chain B: H.41, F.137, M.138, S.139, G.140, S.141, C.142, H.160, H.161, L.162, E.163, L.164, H.169, D.184, E.185, E.186, V.187, Q.189 Ligands: B1S.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.41, B:L.164, B:D.184, B:E.186 Hydrogen bonds: B:G.140, B:S.141, B:C.142, B:H.161, B:E.163, B:E.186, B:E.186, A:A.1

2 x B1S: (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid(Covalent)(Non-covalent)

B1S.2: 15 residues within 4Å: Chain A: H.41, K.45, F.137, M.138, S.139, C.142, H.160, H.161, L.162, E.163, H.169, D.184, E.186 Ligands: K36.1, GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.41, A:K.45, A:D.184, A:E.186 Hydrogen bonds: A:H.161, A:E.163, A:E.163, A:E.186 Water bridges: A:H.41, A:G.140, A:G.140 B1S.6: 18 residues within 4Å: Chain A: A.1 Chain B: H.41, F.137, M.138, S.139, C.142, H.160, H.161, L.162, E.163, L.164, H.169, D.184, E.185, E.186, V.187, Q.189 Ligands: K36.5 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.41, B:L.164, B:D.184, B:E.186 Hydrogen bonds: B:C.142, B:H.161, B:E.163, B:E.186, B:E.186, A:A.1 Water bridges: B:G.140, B:G.140

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.186 Ligands: K36.1, B1S.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.186 Water bridges: A:K.45 GOL.4: 5 residues within 4Å: Chain A: R.128, K.134, A.194, A.196, D.286 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.128 Water bridges: A:A.194, A:A.194, A:D.286, A:D.286, A:E.287, A:E.287 GOL.7: 5 residues within 4Å: Chain B: R.40, G.81, G.176, I.177, F.178 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.40, B:R.40, B:A.82, B:F.178 Water bridges: B:F.178 GOL.8: 4 residues within 4Å: Chain B: R.128, A.194, A.196, D.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.128, B:A.194 Water bridges: B:D.286, B:D.286, B:E.287 GOL.9: 5 residues within 4Å: Chain B: Y.237, K.267, E.268, A.270, D.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.271, B:D.271 GOL.10: 5 residues within 4Å: Chain B: W.215, L.269, G.272, W.273, Y.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zvornicanin, S.N. et al., Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Viruses (2023)

Release Date

2023-03-29

Peptides

main protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

main protease

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