SMTL ID : 6wrz.1

Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 with 7-methyl-GpppA and S-adenosyl-L-homocysteine in the Active Site and Sulfates in the mRNA Binding Groove.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 19 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: GTA.2 10 PLIP interactions: 10 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:F.152

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

GTA.2: 20 residues within 4Å: Chain A: C.28, D.29, L.30, Y.33, K.49, Y.135, T.139, K.140, V.142, K.173, T.175, E.176, H.177, S.178, N.201, S.204, S.205, E.206 Ligands: SAH.1, SO4.4 30 PLIP interactions: 30 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:Y.135, A:K.173, A:T.175, A:H.177, A:S.178, A:N.201, A:S.204, A:S.205 Water bridges: A:K.27, A:K.27, A:D.29, A:N.46, A:K.140, A:K.140, A:N.201, A:S.203, A:S.204 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 MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

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

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: M.45 Ligands: GTA.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.49, A:K.49, A:N.201, A:N.201 SO4.5: 3 residues within 4Å: Chain A: M.44, M.45, K.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.45 Water bridges: A:K.79 Salt bridges: A:K.79 SO4.6: 2 residues within 4Å: Chain A: K.41, G.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.40, A:G.42 Water bridges: A:K.41, A:I.43, A:I.43 SO4.7: 3 residues within 4Å: Chain A: K.41, G.42 Chain B: K.46 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.41, B:K.46 SO4.8: 3 residues within 4Å: Chain A: H.122, T.123, K.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.123, A:T.123 Water bridges: A:K.163 Salt bridges: A:H.122, A:K.163 SO4.9: 8 residues within 4Å: Chain A: R.69, A.124, N.125, K.126, R.286, E.287, N.288, N.289 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.125, A:K.126, A:E.287, A:E.287, A:N.289 Salt bridges: A:R.69 SO4.10: 1 residues within 4Å: Chain A: W.8 No protein-ligand interaction detected (PLIP) SO4.11: 3 residues within 4Å: Chain A: G.34, D.35, S.36 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.35, A:S.36, A:S.36 SO4.17: 4 residues within 4Å: Chain B: Q.56, I.58, T.59, V.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.60 Water bridges: B:T.61 SO4.18: 3 residues within 4Å: Chain B: T.50, T.52, E.63 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.50, B:T.52, B:E.63 Water bridges: B:T.50, A:S.251

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

CL.12: 1 residues within 4Å: Chain A: E.150 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: E.150, G.151 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: H.189 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: D.85, H.86, G.91 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.15: 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.16: 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

Rosas-Lemus, M. et al., High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design. Sci.Signal. (2020)

Release Date

2020-05-13

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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