SMTL ID : 9grq.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TEP: THEOPHYLLINE

TEP.1: 7 residues within 4Å: Chain A: C.25, D.26, L.27, Y.30, K.137, V.139 Ligands: EDO.24 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.26, A:L.27, A:K.137 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24

28 x EDO: 1,2-ETHANEDIOL

EDO.2: 9 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93, L.254 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150 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: 6 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, E.203 Ligands: SAM.16 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: K.24, N.138, V.139, K.141, N.143, E.173, H.174 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: L.22, E.142, N.143 Ligands: EDO.18 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: A.34, T.35, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: V.118, H.119, T.120, F.156, Q.159, K.160 Ligands: EDO.26 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.158, D.179, K.182, H.186 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.4, EDO.19 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: T.117, L.295 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: M.20, L.21 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: E.23, K.24 Ligands: EDO.8 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: A.10, P.12, N.13, W.189 Ligands: MES.4, EDO.14 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: D.102, F.103, T.110, I.112 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: S.145, K.146, E.147 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain A: L.100, D.114 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: K.16, Q.18, I.219, D.220, V.223, M.224, N.227 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Y.30, Y.132, K.137, S.201, S.202 Ligands: TEP.1, NA.27 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: L.262, K.263, E.264, I.267, I.282 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: Y.152, G.155, F.156, Q.159 Ligands: EDO.12 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: D.92, T.112, N.115, W.124 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: R.79, C.80, H.81 Ligands: EDO.36 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain B: M.64 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: H.84, G.89, C.91, K.94 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: N.63, M.64, D.65 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: I.39, R.79, C.80 Ligands: EDO.31 Ligand excluded by PLIP

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID

MES.4: 7 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189 Ligands: EDO.14, EDO.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189 MES.33: 10 residues within 4Å: Chain A: K.38, G.39 Chain B: T.40, N.41, C.42, K.44, E.67, F.69, A.105, P.108 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.38, B:K.44 Hydrogen bonds: B:C.42, B:E.67

2 x NA: SODIUM ION

NA.11: 3 residues within 4Å: Chain A: A.60, M.65, D.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.60, A:A.60, A:S.166 NA.27: 6 residues within 4Å: Chain A: Y.132, T.136, K.137, T.172, H.174 Ligands: EDO.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.136, A:T.172 Water bridges: A:E.173

1 x SAM: S-ADENOSYLMETHIONINE

SAM.16: 20 residues within 4Å: Chain A: N.43, Y.47, 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, F.149, K.170 Ligands: EDO.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.43, A:G.71, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:H.69, A:G.71, A:A.72, A:S.74 Salt bridges: A:D.130

2 x ZN: ZINC ION

ZN.28: 4 residues within 4Å: Chain B: C.75, C.78, H.84, C.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.29: 4 residues within 4Å: Chain B: C.118, C.121, 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

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

2024-09-25

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

Related Entries With Identical Sequence