SMTL ID : 6wq3.1

Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-adenosyl-L-homocysteine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAH.1: 20 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, SO4.9 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:N.104, A:N.104, A:N.104, 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, SO4.9 31 PLIP interactions: 31 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: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:K.27, A:D.29, A:N.46, A:K.140, A:K.140, A:N.201, A:S.204, 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 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:T.61, A:T.61, A:N.213 pi-Stacking: A:W.192, A:W.192

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

SO4.4: 3 residues within 4Å: Chain A: M.44, M.45, K.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.45 Salt bridges: A:K.79 SO4.5: 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 SO4.6: 7 residues within 4Å: Chain A: R.69, N.125, K.126, R.286, E.287, N.288, N.289 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.125, A:K.126, A:K.126, A:E.287, A:N.289, A:N.289 Salt bridges: A:R.69 SO4.7: 5 residues within 4Å: Chain A: K.41, G.42 Chain B: K.46, N.108 Ligands: SO4.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:G.42, A:G.42 Salt bridges: A:K.41, B:K.46 SO4.8: 3 residues within 4Å: Chain A: K.41, G.42 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.42 Water bridges: A:I.43, A:I.43 SO4.9: 3 residues within 4Å: Chain A: N.46 Ligands: SAH.1, GTA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.46, A:N.46 SO4.12: 3 residues within 4Å: Chain B: T.50, T.52, G.53 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:S.251 Hydrogen bonds: B:T.50, B:T.52, B:T.52, B:T.52 SO4.13: 3 residues within 4Å: Chain B: Q.56, T.59, V.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.60

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 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.11: 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

2020-05-06

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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