SMTL ID : 9p6p.2 (1 other biounit)

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x M7G- A- U- U: RNA (5'-D(*(M7G))-R(P*AP*UP*U)-3')(Non-covalent)

M7G-A-U-U.1: 27 residues within 4Å: Chain A: C.28, D.29, L.30, Y.33, S.36, A.37, L.39, M.45, N.46, K.49, S.77, D.78, K.79, 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: SAH.2, SO4.15 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.30, A:Y.33, A:K.140, A:T.175, A:H.177, A:S.178, A:S.205 Salt bridges: A:K.140, A:K.140 pi-Stacking: A:Y.33, A:Y.33 pi-Cation interactions: A:Y.33

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

SAH.2: 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: M7G-A-U-U.1, M7G-A-U-U.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.46, A:Y.50, A:G.74, 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:A.75, A:S.77, A:D.102, A:N.104, A:N.104, A:F.152

1 x MGT: 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

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

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

CL.4: 2 residues within 4Å: Chain A: S.5, W.8 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.149, E.150 Ligands: SO4.13 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: E.26, K.27 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.138, N.141 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.219 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: T.121, K.127 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: T.42, N.43 Ligand excluded by PLIP

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

SO4.9: 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 Water bridges: A:Q.162, A:K.163 Salt bridges: A:H.122, A:K.163 SO4.10: 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:N.289, A:N.289, A:N.289 Salt bridges: A:R.69 SO4.11: 1 residues within 4Å: Chain A: R.22 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.22 SO4.12: 2 residues within 4Å: Chain A: N.289, R.290 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.290 SO4.13: 4 residues within 4Å: Chain A: K.138, E.150, G.151 Ligands: CL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.151 Water bridges: A:D.136, A:T.154 Salt bridges: A:K.138 SO4.14: 3 residues within 4Å: Chain A: P.40, K.41, G.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.42 SO4.15: 2 residues within 4Å: Chain A: K.27 Ligands: M7G-A-U-U.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.27 SO4.20: 3 residues within 4Å: Chain B: Q.56, T.59, V.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.58, B:V.60 SO4.21: 4 residues within 4Å: Chain A: K.41, G.42 Chain B: K.46, A.107 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.41, B:K.46

2 x ZN: ZINC ION(Non-covalent)

ZN.16: 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.17: 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

Minasov, G. et al., Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH). To Be Published

Release Date

2025-07-02

Peptides

2'-O-methyltransferase: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

2'-O-methyltransferase

Non-structural protein 10

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