SMTL ID : 9gtf.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256190

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-1-1-mer

Ligands

12 x EDO: 1,2-ETHANEDIOL

EDO.1: 8 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.133, A:F.149 Water bridges: A:D.133 EDO.3: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.120, A:V.289 EDO.4: 6 residues within 4Å: Chain A: A.34, T.35, L.239, S.240, S.241, Y.242 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.35, A:L.239, A:S.241, A:S.241 EDO.5: 5 residues within 4Å: Chain A: Q.158, D.179, K.182, L.183, H.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.179 EDO.6: 8 residues within 4Å: Chain A: R.66, A.121, N.122, K.123, R.283, E.284, N.285, N.286 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.66, A:R.66, A:K.123, A:E.284, A:E.284, A:E.284, A:N.286 EDO.7: 7 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, I.219, M.224 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.16, A:W.190, A:E.217 EDO.8: 8 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: SAM.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.170, A:N.198, A:S.201, A:E.203 Water bridges: A:K.46 EDO.9: 6 residues within 4Å: Chain A: N.55, T.56, L.57, K.253, R.255 Ligands: MES.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.55 EDO.10: 10 residues within 4Å: Chain A: K.16, M.17, Q.18, Q.218, I.219, D.220, V.223, M.224, N.227 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:D.220, A:D.220 EDO.13: 7 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105 Ligands: EDO.17 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.44, A:K.38 EDO.16: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.113 EDO.17: 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.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.41, B:C.42, B:A.105

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

MES.2: 7 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x SAM: S-ADENOSYLMETHIONINE

SAM.11: 22 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.8 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:G.71, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71 Salt bridges: A:D.130

1 x 01: 7-[(3~{R},4~{R},6~{S})-1-[(2~{S})-2-azanyl-4-methyl-pentanoyl]-4-methyl-4,6-bis(oxidanyl)azepan-3-yl]-1,3-dimethyl-purine-2,6-dione

01.12: 12 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Q.28, Y.30, G.31, K.137, V.139, E.173, S.201, S.202 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.24, A:L.27, A:Y.30, A:K.137 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24, A:K.24

2 x ZN: ZINC ION

ZN.14: 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.15: 5 residues within 4Å: Chain B: C.118, V.120, 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 CL: CHLORIDE ION

CL.18: 2 residues within 4Å: Chain B: I.39, R.79 Ligand excluded by PLIP

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

2024-10-02

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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