SMTL ID : 7jpe.1

Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with m7GpppA Cap-0 and SAM Determined by Fixed-Target Serial Crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.1: 18 residues within 4Å: Chain A: C.28, D.29, L.30, Y.33, K.49, Y.135, P.137, K.140, K.173, T.175, E.176, H.177, S.178, N.201, S.204, S.205, E.206 Ligands: SAM.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:L.30, A:Y.33, A:Y.33, A:K.49, A:K.49, A:Y.135, A:K.173, A:H.177, A:S.178, A:N.201, A:S.205 Water bridges: A:N.46 Salt bridges: A:K.140, A:K.140, A:K.140 pi-Stacking: A:Y.33, A:Y.135 pi-Cation interactions: A:Y.33

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

SAM.2: 18 residues within 4Å: Chain A: N.46, Y.50, G.74, A.75, G.76, S.77, P.83, G.84, D.102, L.103, N.104, D.117, C.118, D.133, M.134, Y.135, F.152 Ligands: GTA.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.46, A:Y.50, A:G.74, A:G.76, A:G.76, A:G.84, A:L.103, A:D.117, A:C.118, A:D.133, A:Y.135 Water bridges: A:G.74, A:S.77, A:D.102, A:N.104 Salt bridges: A:D.133

1 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.3: 7 residues within 4Å: Chain A: L.60, T.61, A.191, W.192, C.212, N.213, S.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.16, A:T.61, A:T.61, A:T.61, A:N.213

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: C.77, C.80, H.86, C.93 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.77, B:C.80, B:H.86, B:C.93 ZN.5: 4 residues within 4Å: Chain B: C.120, C.123, C.131, C.133 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.120, B:C.123, B:C.131, B:C.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilamowski, M. et al., 2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2020-08-26

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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