SMTL ID : 6wvn.1

Crystal Structure of Nsp16-Nsp10 from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-Adenosylmethionine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.258, R.282 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: P.239, Q.241 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: K.149, E.150 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: G.151 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: P.15, N.16, L.17 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: A.37, T.38, L.39 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: L.114, I.115 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: K.144 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: N.271, D.272 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: N.104, D.105 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: K.41 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: T.59, V.60 Ligand excluded by PLIP CL.28: 1 residues within 4Å: Chain A: K.41 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: D.85, H.86, G.91 Ligand excluded by PLIP

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

SAM.12: 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.13, SO4.17 15 PLIP interactions: 15 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:S.77, A:D.102, A:N.104, A:N.104, A:F.152 Salt bridges: A:D.133

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

GTA.13: 19 residues within 4Å: Chain A: C.28, D.29, L.30, Y.33, K.49, Y.135, K.140, V.142, K.173, T.175, E.176, H.177, S.178, N.201, S.204, S.205, E.206 Ligands: SAM.12, SO4.17 27 PLIP interactions: 27 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:N.46, 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.14: 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:N.213 Water bridges: A:N.16

2 x ADE: ADENINE(Non-covalent)

ADE.15: 1 residues within 4Å: Chain A: W.8 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.8 ADE.16: 1 residues within 4Å: Chain A: Y.225 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.225 pi-Stacking: A:Y.225, A:Y.225

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

SO4.17: 3 residues within 4Å: Chain A: N.46 Ligands: SAM.12, GTA.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.46 Water bridges: A:N.46, A:K.49, A:S.77 SO4.18: 3 residues within 4Å: Chain A: M.44, M.45, K.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.45 Water bridges: A:N.46, A:K.79 Salt bridges: A:K.79 SO4.19: 3 residues within 4Å: Chain A: H.122, T.123, K.163 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.123, A:T.123 Water bridges: A:K.163, A:K.163 Salt bridges: A:H.122, A:K.163 SO4.20: 8 residues within 4Å: Chain A: R.69, A.124, 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:E.287, A:E.287, A:N.289, A:N.289 Salt bridges: A:R.69 SO4.21: 2 residues within 4Å: Chain A: K.41, G.42 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.42 Water bridges: A:K.41, A:K.41, A:I.43, A:I.43 SO4.22: 3 residues within 4Å: Chain A: G.34, D.35, S.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.36, A:S.36 SO4.23: 2 residues within 4Å: Chain A: K.280, R.282 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.280, A:R.282 SO4.24: 4 residues within 4Å: Chain A: H.189, G.216, K.217, P.218 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.189 SO4.30: 3 residues within 4Å: Chain A: K.41, G.42 Chain B: K.46 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:K.41, A:K.41, B:A.107 Salt bridges: A:K.41, B:K.46 SO4.31: 2 residues within 4Å: Chain B: T.50, T.52 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.50, B:T.52, B:T.52 Water bridges: B:T.50, B:T.50

2 x ZN: ZINC ION(Non-covalent)

ZN.25: 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.26: 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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