SMTL ID : 8d35.1

Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 3 residues within 4Å: Chain A: I.108, Q.109, Q.112 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 5 residues within 4Å: Chain A: C.24, T.27, V.44, I.45, C.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.27 Water bridges: A:T.27 NA.4: 4 residues within 4Å: Chain B: N.223, F.225, D.265, A.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.223, B:F.225, B:F.225

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.55, D.58, R.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.62 GOL.5: 9 residues within 4Å: Chain A: K.7, A.9, V.127, Y.128, Q.129 Chain B: K.7, V.127, Y.128, Q.129 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.129, B:Q.129, A:Q.129, A:Q.129 GOL.6: 2 residues within 4Å: Chain B: N.182, F.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.183 Water bridges: B:F.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Oliviera, A. et al., Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease. Elife (2023)

Release Date

2023-03-01

Peptides

3C-like proteinase nsp5: AB
tRNA (guanine(26)-N(2))-dimethyltransferase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

3C-like proteinase nsp5

tRNA (guanine(26)-N(2))-dimethyltransferase