SMTL ID : 7jib.1

Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: V.12, A.13 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: M.44, M.45, N.46, K.79 Ligand excluded by PLIP

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

SAM.3: 21 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, G.116, D.117, C.118, D.133, M.134, Y.135, F.152 Ligands: SAH.4, GTA.5, V9G.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.46, A:G.74, A:G.76, A:G.84, A:L.103, A:D.117, A:C.118, A:Y.135 Water bridges: A:G.74, A:D.102, A:N.104, A:N.104 Salt bridges: A:D.133

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 21 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, G.116, D.117, C.118, D.133, M.134, Y.135, F.152 Ligands: SAM.3, GTA.5, V9G.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.46, A:G.74, A:G.76, A:G.84, A:L.103, A:N.104, A:D.117, A:C.118, A:Y.135 Water bridges: A:G.74, A:D.102

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

GTA.5: 20 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.3, SAH.4, V9G.6 22 PLIP interactions: 22 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:T.175, A:E.176, A:H.177, A:S.178, A:N.201, A:S.204, 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.33, A:Y.135 pi-Cation interactions: A:Y.33

1 x V9G: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE(Non-covalent)

V9G.6: 20 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.3, SAH.4, GTA.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:L.30, A:Y.33, A:Y.33, A:K.49, A:Y.135, A:K.173, A:T.175, A:T.175, A:E.176, A:H.177, A:S.178, A:N.201, A:S.204, A:S.205 Water bridges: A:K.27, A:N.46 Salt bridges: A:D.29, A:K.140, A:K.140, A:K.140 pi-Stacking: A:Y.33, A:Y.33, A:Y.135

1 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.7: 8 residues within 4Å: Chain A: N.16, L.60, T.61, A.191, W.192, C.212, N.213, S.279 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.16, A:T.61, A:T.61, A:N.213 Water bridges: A:N.16 pi-Stacking: A:W.192, A:W.192

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 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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