SMTL ID : 6w61.1

Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.20, D.221, M.225 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: D.134, T.137, K.147, E.148, G.149, F.150, F.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.137, A:T.137, A:E.148, A:F.150 Water bridges: A:D.134 EDO.3: 4 residues within 4Å: Chain A: N.44, K.47, K.171 Ligands: SAM.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.44, A:E.204 Water bridges: A:K.47, A:K.47, A:K.171 EDO.5: 3 residues within 4Å: Chain B: T.112, L.113, N.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.113

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.4: 19 residues within 4Å: Chain A: N.44, Y.48, G.72, A.73, G.74, S.75, P.81, G.82, D.100, L.101, N.102, G.114, D.115, C.116, D.131, M.132, Y.133, F.150 Ligands: EDO.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.44, A:Y.48, A:G.72, A:G.74, A:G.82, A:L.101, A:N.102, A:D.115, A:C.116, A:D.131, A:Y.133 Water bridges: A:G.74, A:D.100 Salt bridges: A:D.131

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.118, C.121, C.129, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.118, B:C.121, B:C.129, B:C.131 ZN.7: 4 residues within 4Å: Chain B: C.75, C.78, H.84, C.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosas-Lemus, M. et al., The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. Biorxiv (2020)

Release Date

2020-03-25

Peptides

2'-O-methyltransferase: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase

Non-structural protein 10

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