SMTL ID : 9gs4.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571130

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93 Ligand excluded by PLIP EDO.2: 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.4: 6 residues within 4Å: Chain A: H.119, T.120, A.121, I.290, S.291 Chain C: D.293 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: K.170, N.198, S.201, E.203 Ligands: EDO.8 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: K.24, V.139, K.141, E.173, H.174 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: A.34, T.35, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: Y.30, Y.132, K.137, S.201, S.202 Ligands: EDO.5, 01.16 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: T.35, L.36, K.38 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.38, G.39 Chain B: K.26 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: H.119, T.120, F.156, Q.159, K.160 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: 4 residues within 4Å: Chain A: T.117, D.293, L.295 Chain C: R.287 Ligand excluded by PLIP EDO.15: 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.21: 4 residues within 4Å: Chain B: D.74, T.94, L.95, N.97 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.61, H.63 Ligands: IMD.24 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain B: M.46 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: D.133, T.136, K.146, E.147, G.148, F.149, F.150 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: D.293 Chain C: H.119, T.120, A.121, I.290, S.291 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain C: K.170, N.198, S.201, E.203 Ligands: EDO.32 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: K.24, V.139, K.141, E.173, H.174 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain C: A.34, T.35, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: Y.30, Y.132, K.137, S.201, S.202 Ligands: EDO.29, 01.40 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: T.35, L.36, K.38 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain C: K.38, G.39 Chain D: K.26 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: H.119, T.120, F.156, Q.159, K.160 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain C: Q.158, D.179, K.182, H.186 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain A: R.287 Chain C: T.117, D.293, L.295 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain C: R.66, N.122, K.123, R.283, E.284, N.285, N.286 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain D: D.74, T.94, L.95, N.97 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain D: R.61, H.63 Ligands: IMD.48 Ligand excluded by PLIP EDO.47: 1 residues within 4Å: Chain D: M.46 Ligand excluded by PLIP

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

MES.3: 5 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189 MES.27: 5 residues within 4Å: Chain C: N.13, T.56, L.57, T.58, W.189 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.13, C:T.58, C:W.189

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

NA.10: 4 residues within 4Å: Chain A: A.60, M.65, D.125, S.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.60, A:D.125, A:S.166 NA.18: 5 residues within 4Å: Chain A: Y.132, T.136, K.137, T.172, H.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.136, A:T.172 NA.34: 4 residues within 4Å: Chain C: A.60, M.65, D.125, S.166 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.60, C:D.125, C:S.166 NA.42: 5 residues within 4Å: Chain C: Y.132, T.136, K.137, T.172, H.174 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.132, C:Y.132, C:T.136

2 x 01: ~{N}-[(5~{S})-5-azanyl-6-[(3~{S},4~{S},6~{R})-3-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]-4-methyl-4,6-bis(oxidanyl)azepan-1-yl]-6-oxidanylidene-hexyl]ethanamide

01.16: 9 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.137, E.173, S.202 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.24, A:L.27, A:Y.30 pi-Stacking: A:Y.30, A:Y.30 01.40: 9 residues within 4Å: Chain C: K.24, C.25, D.26, L.27, Y.30, K.137, E.173, S.202 Ligands: EDO.32 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.24, C:D.26, C:L.27 pi-Stacking: C:Y.30, C:Y.30

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

SAM.17: 19 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 13 PLIP interactions: 13 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:G.71, A:G.73, A:D.99 Salt bridges: A:D.130 SAM.41: 19 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:N.43, C:Y.47, C:G.71, C:G.73, C:G.81, C:L.100, C:N.101, C:D.114, C:C.115, C:D.130, C:Y.132 Water bridges: C:G.71, C:G.73, C:D.99 Salt bridges: C:D.130

4 x ZN: ZINC ION(Non-covalent)

ZN.19: 4 residues within 4Å: Chain B: C.57, C.60, H.66, C.73 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.57, B:C.60, B:H.66, B:C.73 ZN.20: 4 residues within 4Å: Chain B: C.100, C.103, C.111, C.113 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.100, B:C.103, B:C.111, B:C.113 ZN.43: 4 residues within 4Å: Chain D: C.57, C.60, H.66, C.73 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.57, D:C.60, D:H.66, D:C.73 ZN.44: 4 residues within 4Å: Chain D: C.100, C.103, C.111, C.113 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.100, D:C.103, D:C.111, D:C.113

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.24: 5 residues within 4Å: Chain B: I.21, R.61, C.62 Chain D: F.2 Ligands: EDO.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.61 Water bridges: B:R.61, B:R.61 IMD.48: 5 residues within 4Å: Chain B: F.2 Chain D: I.21, R.61, C.62 Ligands: EDO.46 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.61 Water bridges: D:R.61, D:R.61

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

2024-10-16

Peptides

2'-O-methyltransferase nsp16: AC
Non-structural protein 10: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

2'-O-methyltransferase nsp16

Non-structural protein 10