SMTL ID : 7lfp.1

SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 6 residues within 4Å: Chain A: E.17, G.18, M.20, V.21, W.34, A.73 No protein-ligand interaction detected (PLIP) DMS.3: 2 residues within 4Å: Chain A: R.43, N.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.43 Water bridges: A:R.43, A:R.43 DMS.4: 7 residues within 4Å: Chain A: M.20, Q.22, Q.72, G.74, N.122, G.123, S.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.74 DMS.5: 5 residues within 4Å: Chain A: L.274, L.275, G.278, M.279, L.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.279 DMS.7: 3 residues within 4Å: Chain A: M.9, F.11 Chain B: S.126 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.11 DMS.11: 5 residues within 4Å: Chain A: S.126 Chain B: M.9, F.11, Q.130, R.301 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.11

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

PEG.2: 3 residues within 4Å: Chain A: Q.22, L.70, N.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.24, A:N.122 PEG.8: 4 residues within 4Å: Chain A: K.140, E.293 Chain B: F.6, R.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.140 PEG.9: 6 residues within 4Å: Chain B: I.81, G.82, H.83, S.84, K.91, K.93 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.83 PEG.10: 4 residues within 4Å: Chain B: E.17, G.18, M.20, K.100 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.100

1 x XY4: N-phenyl-N'-propan-2-ylurea(Non-covalent)

XY4.6: 9 residues within 4Å: Chain A: R.7, K.8, A.10, V.128, Y.129, Q.130 Chain B: K.8, A.10, Q.130 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:R.7, A:Q.130, B:Q.130 Hydrogen bonds: A:R.7, B:Q.130, B:Q.130, B:Q.130

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

2021-02-03

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

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