SMTL ID : 7kvl.1

SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

11 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.2: 5 residues within 4Å: Chain A: Q.22, T.29, L.70, Q.72, N.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.72, A:N.122 PEG.4: 5 residues within 4Å: Chain A: G.82, H.83, S.84, K.91, K.93 No protein-ligand interaction detected (PLIP) PEG.5: 7 residues within 4Å: Chain A: E.17, G.18, M.20, W.34, A.73, N.98, K.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.100 PEG.6: 2 residues within 4Å: Chain A: F.226, T.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.227 PEG.7: 3 residues within 4Å: Chain A: N.183, F.184, G.186 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.108, A:F.184 PEG.8: 5 residues within 4Å: Chain A: P.187, R.191, T.193, A.194, Q.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.187, A:R.191 PEG.14: 6 residues within 4Å: Chain A: R.134, K.140, E.293 Chain B: S.4, R.7 Ligands: DMS.20 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.4, B:S.4, B:R.7, B:R.7, A:K.140 Water bridges: A:K.8 PEG.16: 4 residues within 4Å: Chain B: E.17, G.18, M.20, K.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.100 PEG.17: 6 residues within 4Å: Chain B: M.20, Q.22, Q.72, G.74, N.122, G.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.74, B:G.123 PEG.18: 3 residues within 4Å: Chain B: Y.242, L.274, L.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.290 Water bridges: B:Y.242

1 x X4P: 2-chloropyridine-4-carboxamide(Non-covalent)

X4P.3: 4 residues within 4Å: Chain A: V.236, Y.240, K.272, Q.276 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.236, A:K.272

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.9: 10 residues within 4Å: Chain A: K.8, A.10, V.128, Y.129, Q.130 Chain B: K.8, M.9, A.10, Y.129, Q.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.10, A:Q.130 DMS.10: 3 residues within 4Å: Chain A: R.43, N.87, C.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.43 Water bridges: A:R.43, A:N.87 DMS.11: 5 residues within 4Å: Chain A: Q.22, Q.72, G.74, N.122, G.123 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.74 DMS.12: 3 residues within 4Å: Chain A: L.274, G.278, M.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.279 DMS.13: 5 residues within 4Å: Chain A: M.9, A.10, F.11 Chain B: S.126, G.127 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.9 pi-Cation interactions: A:F.11 DMS.19: 6 residues within 4Å: Chain A: S.126 Chain B: M.9, A.10, F.11, Q.130, R.301 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.11 DMS.20: 3 residues within 4Å: Chain B: R.7, K.8 Ligands: PEG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.7 DMS.21: 3 residues within 4Å: Chain B: R.108, F.184, G.186 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.108

1 x SER: SERINE(Non-covalent)

SER.15: 3 residues within 4Å: Chain B: V.300, R.301, C.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noske, G.D. et al., A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process. J.Mol.Biol. (2021)

Release Date

2020-12-09

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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