SMTL ID : 7lfe.1

SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 2 residues within 4Å: Chain A: Q.22, L.70 No protein-ligand interaction detected (PLIP) PEG.7: 5 residues within 4Å: Chain B: G.82, H.83, S.84, K.91, K.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.93 PEG.9: 5 residues within 4Å: Chain A: K.140, E.293 Chain B: F.6, R.7, L.285 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.140, B:F.6 PEG.11: 5 residues within 4Å: Chain B: G.18, W.34, A.73, N.98, K.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.98, B:K.100

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

DMS.2: 3 residues within 4Å: Chain A: R.43, N.87, C.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.43 DMS.3: 5 residues within 4Å: Chain A: Q.22, Q.72, G.74, N.122, G.123 No protein-ligand interaction detected (PLIP) DMS.4: 4 residues within 4Å: Chain A: L.275, G.278, M.279, L.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.279 DMS.5: 4 residues within 4Å: Chain A: M.9, F.11, D.298, R.301 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.11 DMS.8: 3 residues within 4Å: Chain A: S.126 Chain B: M.9, R.301 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.11 DMS.10: 5 residues within 4Å: Chain A: K.8, A.10 Chain B: K.8, V.128, Q.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.10, A:Q.130

1 x XWS: (2R,4R)-1-phenylhexahydropyrimidine-2,4-diol(Non-covalent)

XWS.6: 8 residues within 4Å: Chain A: H.44, M.52, C.148, H.167, M.168, E.169, D.190, Q.192 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.44, A:M.168, A:Q.192 Hydrogen bonds: A:E.169 pi-Cation interactions: A:H.44

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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