SMTL ID : 9gny.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

20 x EDO: 1,2-ETHANEDIOL

EDO.1: 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.2: 9 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 Ligands: SAM.17 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: EDO.9, SAM.17 Ligand excluded by PLIP EDO.6: 10 residues within 4Å: Chain A: K.24, C.25, N.138, V.139, K.141, E.142, N.143, E.173, H.174 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: L.22, E.23, K.24, E.142, N.143 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: S.33, A.34, T.35, L.239, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: Y.132, K.137, T.172, E.173, S.201, S.202, E.203 Ligands: EDO.5, CFF.16 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.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.3 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: 8 residues within 4Å: Chain A: R.66, N.122, K.123, R.283, E.284, N.285, N.286, R.287 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligands: EDO.27 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, K.114, N.115, T.116, V.117, W.124 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: 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: 6 residues within 4Å: Chain A: K.76 Chain B: I.39, T.40, N.41, R.79 Ligands: IMD.25 Ligand excluded by PLIP EDO.27: 10 residues within 4Å: Chain B: I.39, T.40, N.41, C.42, F.69, A.105, N.106, D.107, P.108 Ligands: EDO.19 Ligand excluded by PLIP

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

MES.3: 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

1 x CFF: CAFFEINE

CFF.16: 11 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.137, V.139, E.173, S.201, S.202 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.27, A:K.137 Water bridges: A:S.202 pi-Stacking: A:Y.30, A:Y.30

1 x SAM: S-ADENOSYLMETHIONINE

SAM.17: 23 residues within 4Å: Chain A: N.43, 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.2, EDO.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:D.130, A:Y.132 Water bridges: A:S.74, A:S.74, A:D.99 Salt bridges: A:D.130

1 x CL: CHLORIDE ION

CL.18: 5 residues within 4Å: Chain A: L.163, L.262, E.264, I.267, I.282 Ligand excluded by PLIP

2 x ZN: ZINC ION

ZN.20: 5 residues within 4Å: Chain B: C.75, Y.77, 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.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

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

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