SMTL ID : 9fwt.1

Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VSL: methyl 4,5,6,7-tetrahydro-2H-indazole-3-carboxylate(Non-covalent)

VSL.1: 8 residues within 4Å: Chain A: D.91, L.92, T.111, N.114, T.115, V.116, T.118, W.123 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.92, A:W.123, A:W.123 Hydrogen bonds: A:D.91, A:V.116

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

DMS.2: 5 residues within 4Å: Chain A: Y.30, S.33, G.35 Chain B: Y.65, Q.66 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.74, A:C.77, A:H.83, A:C.90 ZN.4: 5 residues within 4Å: Chain A: C.117, C.120, C.128, S.129, C.130 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.117, A:C.120, A:C.128, A:C.130 ZN.5: 4 residues within 4Å: Chain B: H.258, C.262, H.265, C.280 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.258, B:C.262, B:H.265, B:C.280 ZN.6: 4 residues within 4Å: Chain B: C.208, C.211, C.227, H.230 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.208, B:C.211, B:C.227, B:H.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krojer, T. et al., Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259. To Be Published

Release Date

2025-07-09

Peptides

Non-structural protein 10: A
Guanine-N7 methyltransferase nsp14: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Non-structural protein 10

Guanine-N7 methyltransferase nsp14

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