SMTL ID : 7kvr.1

SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 8 residues within 4Å: Chain A: E.17, G.18, M.20, W.34, A.73, G.74, N.98, K.100 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: L.274, L.275, G.278, M.279 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.279 DMS.7: 4 residues within 4Å: Chain A: F.11, D.298, Q.302 Chain B: S.126 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.130 Salt bridges: A:D.298 DMS.9: 8 residues within 4Å: Chain A: K.8, A.10, V.128 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 Water bridges: A:Q.130 DMS.11: 6 residues within 4Å: Chain A: S.126 Chain B: M.9, F.11, Q.130, R.301, Q.302 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.11 DMS.12: 8 residues within 4Å: Chain B: V.117, A.119, Y.129, G.141, S.142, L.144, S.147, S.150 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.129, B:S.147, B:S.150 pi-Cation interactions: B:H.175

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: 5 residues within 4Å: Chain A: Q.22, T.24, L.70, Q.72, N.122 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain A: C.25, G.26, T.27, I.46, C.47, K.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.27, A:C.47, A:N.68 PEG.5: 5 residues within 4Å: Chain A: G.82, H.83, S.84, K.91, K.93 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain A: K.8, E.291, E.293 Chain B: R.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.8, A:E.291

1 x X4V: N~4~,N~4~-dimethylpyridine-2,4-diamine(Non-covalent)

X4V.10: 2 residues within 4Å: Chain B: Q.86, N.87 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.86

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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