SMTL ID : 7kok.1

The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496 inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x Y96: 5-[(E)-(hydroxyimino)methyl]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide(Non-covalent)

Y96.1: 10 residues within 4Å: Chain A: L.165, G.166, D.167, P.250, P.251, Y.267, Y.271, Q.272, Y.276, T.304 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:D.167, A:P.250, A:P.251, A:Y.267, A:Y.267, A:Y.271, A:Y.271, A:Q.272, A:T.304 Hydrogen bonds: A:D.167, A:Y.271, A:Q.272, A:Q.272, A:Y.276 pi-Stacking: A:Y.271, A:Y.271

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.192, C.195, C.227, C.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.227, A:C.229 ZN.3: 3 residues within 4Å: Chain A: H.20, T.66, E.70 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.20, A:E.70, A:E.70 ZN.4: 2 residues within 4Å: Chain A: H.92, D.111 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:D.111, H2O.7 ZN.5: 4 residues within 4Å: Chain A: H.76, N.131 Ligands: CL.7, CL.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.76

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

CL.6: 6 residues within 4Å: Chain A: T.13, V.14, D.15, N.18, H.20, E.70 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain A: H.76, N.131, P.132, H.178 Ligands: ZN.5, CL.8, UNX.15 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.76 Ligands: ZN.5, CL.7 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 7 residues within 4Å: Chain A: W.109, N.112, N.113, S.114, L.165, G.274, H.275 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.112, A:L.165 Hydrogen bonds: A:N.112, A:S.114, A:S.114 Salt bridges: A:H.275

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.10: 3 residues within 4Å: Chain A: A.42, D.43, N.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.43, A:N.91

13 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.11: 3 residues within 4Å: Chain A: Q.177 Ligands: UNX.12, UNX.14 No protein-ligand interaction detected (PLIP) UNX.12: 5 residues within 4Å: Chain A: H.178 Ligands: UNX.11, UNX.13, UNX.14, UNX.15 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain A: Y.157, H.178 Ligands: UNX.12, UNX.15 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain A: Q.177, H.178 Ligands: UNX.11, UNX.12 No protein-ligand interaction detected (PLIP) UNX.15: 5 residues within 4Å: Chain A: H.76, H.178 Ligands: CL.7, UNX.12, UNX.13 No protein-ligand interaction detected (PLIP) UNX.16: 5 residues within 4Å: Chain A: H.258 Ligands: UNX.18, UNX.19, UNX.21, UNX.22 No protein-ligand interaction detected (PLIP) UNX.17: 6 residues within 4Å: Chain A: H.258, E.283 Ligands: UNX.19, UNX.20, UNX.21, UNX.23 No protein-ligand interaction detected (PLIP) UNX.18: 5 residues within 4Å: Chain A: H.258 Ligands: UNX.16, UNX.19, UNX.21, UNX.22 No protein-ligand interaction detected (PLIP) UNX.19: 8 residues within 4Å: Chain A: H.258 Ligands: UNX.16, UNX.17, UNX.18, UNX.20, UNX.21, UNX.22, UNX.23 No protein-ligand interaction detected (PLIP) UNX.20: 4 residues within 4Å: Ligands: UNX.17, UNX.19, UNX.21, UNX.23 No protein-ligand interaction detected (PLIP) UNX.21: 8 residues within 4Å: Chain A: H.258 Ligands: UNX.16, UNX.17, UNX.18, UNX.19, UNX.20, UNX.22, UNX.23 No protein-ligand interaction detected (PLIP) UNX.22: 6 residues within 4Å: Chain A: H.258 Ligands: UNX.16, UNX.18, UNX.19, UNX.21, UNX.23 No protein-ligand interaction detected (PLIP) UNX.23: 6 residues within 4Å: Chain A: H.258 Ligands: UNX.17, UNX.19, UNX.20, UNX.21, UNX.22 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with PLP_Snyder496. to be published

Release Date

2020-11-18

Peptides

Papain-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Papain-like protease

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