SMTL ID : 7kfi.1

SARS-CoV-2 Main protease immature form - apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 7 residues within 4Å: Chain A: E.17, G.18, M.20, V.21, W.34, A.73, K.100 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.100 DMS.6: 10 residues within 4Å: Chain A: K.8, M.9, A.10, V.128 Chain B: K.8, M.9, A.10, V.128, Y.129, Q.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.10 Water bridges: A:Q.130 DMS.7: 2 residues within 4Å: Chain A: R.43, N.87 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.43, A:R.43, A:R.43 DMS.8: 6 residues within 4Å: Chain A: Q.22, Q.72, G.74, N.122, G.123, S.124 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.74 DMS.9: 4 residues within 4Å: Chain A: L.274, L.275, G.278, M.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.279 DMS.10: 2 residues within 4Å: Chain A: F.11, D.298 No protein-ligand interaction detected (PLIP) DMS.12: 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

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

PEG.2: 1 residues within 4Å: Chain A: E.50 No protein-ligand interaction detected (PLIP) PEG.3: 4 residues within 4Å: Chain A: Q.22, T.24, T.29, L.70 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.122 PEG.4: 4 residues within 4Å: Chain A: R.134, K.140, E.293 Chain B: R.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.140 PEG.5: 5 residues within 4Å: Chain A: G.82, H.83, S.84, K.91, K.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.83, A:K.91, A:K.93 PEG.11: 4 residues within 4Å: Chain B: E.17, G.18, M.20, K.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.100 Water bridges: B:G.18, B:N.98, B:K.100

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

2020-10-28

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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