SMTL ID : 7c2i.1

Crystal structure of nsp16-nsp10 heterodimer from SARS-CoV-2 in complex with SAM (with additional SAM during crystallization)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: N.50, Y.54, G.78, A.79, G.80, S.81, P.87, G.88, D.106, L.107, N.108, G.120, D.121, C.122, D.137, M.138, Y.139, F.156 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.50, A:Y.54, A:G.78, A:G.80, A:G.88, A:L.107, A:D.121, A:C.122, A:D.137, A:Y.139 Water bridges: A:G.78, A:S.81, A:N.108, A:N.108 Salt bridges: A:D.137

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: C.122, C.125, C.133, C.135 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.122, B:C.125, B:C.133, B:C.135 ZN.3: 4 residues within 4Å: Chain B: C.79, C.82, H.88, C.95 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.79, B:C.82, B:H.88, B:C.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, S. et al., Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-O-methylase and its implication on antiviral drug design. Signal Transduct Target Ther (2020)

Release Date

2020-05-27

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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