SMTL ID : 9fwk.1

Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 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

1 x 01: (4S)-4-pyridin-4-ylpyrrolidin-2-one

01.3: 14 residues within 4Å: Chain A: N.3, A.4, T.5 Chain B: D.11, I.16, T.17, G.18, L.19, L.28, S.29, V.30, D.31, T.32, R.54 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.11, B:I.16, B:T.32 Hydrophobic interactions: A:N.3

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

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

1 x 02: (4R)-4-pyridin-4-ylpyrrolidin-2-one

02.7: 6 residues within 4Å: Chain B: W.87, I.88, S.113, T.114, L.178, R.279 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:R.279

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 VT00123. To Be Published

Release Date

2025-08-20

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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