SMTL ID : 7ldx.1

SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.2: 4 residues within 4Å: Chain A: Q.22, T.29, L.70, N.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.122 PEG.3: 5 residues within 4Å: Chain A: R.134, K.140, E.293 Chain B: F.6, R.7 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.293, B:F.6, B:R.7, B:R.7

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

DMS.4: 10 residues within 4Å: Chain A: K.8, M.9, A.10, V.128, 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.5: 2 residues within 4Å: Chain A: R.43, N.87 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.43 DMS.6: 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 Hydrogen bonds: A:G.74 DMS.7: 4 residues within 4Å: Chain A: L.274, G.278, M.279, L.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.279 DMS.8: 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.10: 6 residues within 4Å: Chain A: S.126 Chain B: M.9, F.11, Q.130, D.298, R.301 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.301 pi-Cation interactions: B:F.11

2 x R9V: (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol(Non-covalent)

R9V.9: 8 residues within 4Å: Chain A: P.135, N.136, T.199, T.201, M.238, Y.242, E.243, P.244 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.135, A:T.201, A:M.238 Hydrogen bonds: A:P.135 Salt bridges: A:E.243 R9V.11: 8 residues within 4Å: Chain B: P.135, N.136, T.199, T.201, M.238, Y.242, E.243, P.244 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.135, B:T.201 Hydrogen bonds: B:P.135 Salt bridges: B:E.243

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

2021-01-20

Peptides

3C-like proteinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3C-like proteinase

Related Entries With Identical Sequence