SMTL ID : 7orv.1

Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00239

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.68, C.71, H.77, C.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.68, A:C.71, A:H.77, A:C.84 ZN.2: 4 residues within 4Å: Chain A: C.111, C.114, C.122, C.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.122, A:C.124

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

DMS.3: 8 residues within 4Å: Chain A: T.1, M.2, G.3, N.4, V.7, Q.30, P.31, T.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.2, A:G.3 DMS.4: 2 residues within 4Å: Chain A: C.73, H.74 No protein-ligand interaction detected (PLIP)

1 x X4V: N~4~,N~4~-dimethylpyridine-2,4-diamine(Non-covalent)

X4V.5: 3 residues within 4Å: Chain A: H.42, M.57, E.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:T.95 pi-Stacking: A:H.42

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: F.10, A.20, D.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.23, A:D.23 Water bridges: A:V.15

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

CL.7: 2 residues within 4Å: Chain A: A.14, V.15 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: Q.59, P.94, W.117, Y.120, G.121 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: M.2, G.3, S.5, T.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozielski, F. et al., Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. Rsc Chem Biol (2022)

Release Date

2021-10-20

Peptides

Non-structural protein 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-structural protein 10

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