SMTL ID : 8c0g.1

SARS-CoV nsp16-nsp10 complexed with N7-GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: D.220, Y.222, T.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.223, A:T.223, A:T.223, A:T.223 PEG.3: 8 residues within 4Å: Chain A: L.27, N.29, Y.132, V.139, T.172, E.173, H.174, S.202 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.29, A:Y.132, A:T.172, A:H.174 Water bridges: A:S.202

1 x SRC: [[(2~{R},3~{S},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

SRC.2: 8 residues within 4Å: Chain A: T.56, L.57, T.58, S.188, W.189, A.209, N.210, E.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.58, A:T.58, A:S.188, A:N.210 pi-Stacking: A:W.189, A:W.189

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 8 residues within 4Å: Chain A: A.60, G.164, N.210, L.274, L.275, G.278, R.279, L.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:L.274, A:L.280

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain B: C.65, C.68, H.74, C.81 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:C.68, B:H.74, B:C.81 ZN.6: 4 residues within 4Å: Chain B: C.108, C.111, C.119, C.121 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.108, B:C.111, B:C.119, B:C.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferron, F. et al., Observation of N7-GTP in nsp16-nsp10 Sars-CoV. To Be Published

Release Date

2023-12-27

Peptides

Non-structural protein 7: A
Non-structural protein 7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Non-structural protein 7

Non-structural protein 7

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