SMTL ID : 7qif.1

Crystal structure of SARS-CoV-2 NSP14 in complex with 7MeGpppG.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x GTG: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE(Non-covalent)

GTG.1: 14 residues within 4Å: Chain A: L.299, N.302, C.305, R.306, P.351, N.382, F.397, Y.416, N.418, K.419, H.420, F.422, T.424, F.502 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.302, A:N.302, A:N.382, A:Y.416, A:K.419, A:T.424, A:T.424 Water bridges: A:T.424 Salt bridges: A:R.306, A:R.306, A:K.419, A:K.419, A:K.419 pi-Stacking: A:F.422, A:F.422

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.253, C.257, H.260, C.275 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.253, A:C.257, A:H.260, A:C.275 ZN.3: 4 residues within 4Å: Chain A: C.448, C.473, C.480, H.483 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.448, A:C.473, A:C.480, A:H.483 ZN.4: 4 residues within 4Å: Chain A: C.203, C.206, C.222, H.225 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.203, A:C.206, A:C.222, A:H.225

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: R.77, H.78, R.80, L.173, S.174, D.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.173, A:D.175, A:D.175, A:D.175 Salt bridges: A:H.78 PO4.6: 6 residues within 4Å: Chain A: Y.442, S.444, S.446, H.482, H.483, E.486 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.442, A:S.444, A:S.444, A:S.444, A:S.446 Salt bridges: A:H.482

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imprachim, N. et al., Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development. Nucleic Acids Res. (2023)

Release Date

2022-02-02

Peptides

Proofreading exoribonuclease nsp14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Proofreading exoribonuclease nsp14

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