SMTL ID : 7orr.1

Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00022

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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: 9 residues within 4Å: Chain A: T.1, M.2, G.3, N.4, V.7, Y.24, Q.30, P.31, T.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.2, A:G.3 DMS.4: 3 residues within 4Å: Chain A: C.73, H.74, I.75 No protein-ligand interaction detected (PLIP)

2 x PIM: 4-PHENYL-1H-IMIDAZOLE(Non-covalent)

PIM.5: 3 residues within 4Å: Chain A: T.6, S.9, F.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.6 PIM.6: 5 residues within 4Å: Chain A: H.42, M.57, Q.59, E.60, T.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:T.95 pi-Stacking: A:H.42

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: C.35, V.36, K.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.35, A:K.37 GOL.8: 4 residues within 4Å: Chain A: T.105, L.106, N.108, W.117 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.106, A:N.108 Water bridges: A:T.105, A:T.105

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

CL.9: 5 residues within 4Å: Chain A: Q.59, P.94, W.117, Y.120, G.121 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: N.4, N.34 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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