SMTL ID : 7r2v.1 (1 other biounit)

Structure of nsp14 from SARS-CoV-2 in complex with SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 16 residues within 4Å: Chain A: W.292, R.310, Q.313, G.333, P.335, D.352, A.353, L.366, F.367, Y.368, W.385, N.386, C.387, V.389, F.426 Ligands: PEG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.313, A:A.353, A:Y.368, A:Y.368, A:W.385 Salt bridges: A:R.310

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

PEG.2: 5 residues within 4Å: Chain A: N.386, Y.420, F.426, T.428 Ligands: SAH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.310, A:N.386, A:T.428 Water bridges: A:N.388

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 2 residues within 4Å: Chain A: C.208, Y.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.224, A:Y.224

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.452, A:C.477, A:C.484, A:H.487 ZN.5: 4 residues within 4Å: Chain A: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.207, A:C.210, A:C.226, A:H.229 ZN.6: 4 residues within 4Å: Chain A: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.257, A:C.261, A:H.264, A:C.279 ZN.7: 2 residues within 4Å: Chain A: S.112, R.278 No protein-ligand interaction detected (PLIP) ZN.8: 4 residues within 4Å: Chain A: P.443, F.444, F.445, Y.494 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czarna, A. et al., Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity. Structure (2022)

Release Date

2022-03-09

Peptides

Proofreading exoribonuclease nsp14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proofreading exoribonuclease nsp14

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