SMTL ID : 9grp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE

SAM.1: 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.19 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.71, A:G.73, 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:A.116 Salt bridges: A:D.130

21 x EDO: 1,2-ETHANEDIOL

EDO.2: 7 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, T.91, G.92, T.93 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, K.170, N.198, S.201, E.203 Ligands: EDO.10 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: 2 residues within 4Å: Chain A: E.23, K.24 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: 6 residues within 4Å: Chain A: Y.132, K.137, S.201, S.202 Ligands: EDO.6, 01.18 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.35, L.36, K.38 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, A.105 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: V.118, H.119, T.120, F.156, Q.159, K.160 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.4 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: T.117, D.293, L.295 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: R.66, N.122, K.123, R.283, E.284, N.285, N.286 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: G.73, S.74, D.99, N.101, D.102, F.103 Ligands: SAM.1 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: N.101, D.102, I.112 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: L.163, L.262, K.263, E.264, I.267, I.282 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: D.92, T.112, N.115 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain B: M.64 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: I.39, T.40, N.41, R.79 Ligands: IMD.26 Ligand excluded by PLIP

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

MES.4: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189 Ligands: EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x 01: 7-(2-chloroethyl)-1,3-dimethyl-purine-2,6-dione

01.18: 9 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.137, V.139, E.173 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.27, A:K.137 pi-Stacking: A:Y.30, A:Y.30

2 x ZN: ZINC ION

ZN.22: 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.23: 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

1 x IMD: IMIDAZOLE

IMD.26: 3 residues within 4Å: Chain B: I.39, R.79 Ligands: EDO.27 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

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