SMTL ID : 9q8h.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative BDH 34019023

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 24 residues within 4Å: Chain A: N.43, K.46, Y.47, H.69, G.71, A.72, G.73, S.74, P.80, G.81, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, D.133, F.149, K.170 Ligands: EDO.3, EDO.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:G.71, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:A.72, A:F.149 Salt bridges: A:D.130

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 10 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93, L.94, L.254 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 Ligands: SAM.1 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: SAM.1, EDO.8 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: S.33, A.34, T.35, Q.238, L.239, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.8: 13 residues within 4Å: Chain A: L.27, Y.30, Y.132, K.137, T.172, E.173, S.200, S.201, S.202, E.203 Ligands: EDO.6, NA.16, 01.17 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: T.35, L.36, K.38 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.4 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: T.117, D.293, V.294, L.295 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain A: R.86, Q.87, W.88, L.89, P.90, T.91, P.251 Chain B: V.58, T.59, Y.97 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligand excluded by PLIP EDO.22: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: K.76, G.77 Chain B: R.79, C.80, H.81 Ligands: IMD.25 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain B: M.64 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: K.76 Chain B: P.38, I.39, T.40, N.41, R.79 Ligands: IMD.25 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 7 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

2 x NA: SODIUM ION(Non-functional Binders)

NA.10: 7 residues within 4Å: Chain A: L.59, A.60, M.65, D.125, L.126, G.165, S.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.60, A:A.60, A:S.166 NA.16: 6 residues within 4Å: Chain A: K.137, T.172, E.173, H.174, S.202 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.172, A:E.173, A:H.174, A:S.202

1 x 01: 9-[(3~{R},4~{R})-1-(3-azanylpropanoyl)-4-oxidanyl-pyrrolidin-3-yl]-1,3-dimethyl-purine-2,6-dione

01.17: 11 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.137, V.139, E.173, H.174, S.202 Ligands: EDO.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.27, A:K.137 Water bridges: A:K.24, A:C.25 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24

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

CL.18: 5 residues within 4Å: Chain A: R.19, I.219, D.220, V.223, M.224 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.20: 6 residues within 4Å: Chain B: C.75, Y.77, C.78, H.84, C.91, K.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.21: 6 residues within 4Å: Chain B: C.118, V.120, C.121, K.125, C.129, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.118, B:C.121, B:C.129, B:C.131

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.25: 5 residues within 4Å: Chain B: I.39, R.79, C.80 Ligands: EDO.23, EDO.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.79 Water bridges: B:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kremling, V. et al., Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders. To Be Published

Release Date

2025-04-02

Peptides

2'-O-methyltransferase nsp16: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase nsp16

Non-structural protein 10

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