SMTL ID : 9guf.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571106

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

25 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 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligand excluded by PLIP EDO.4: 9 residues within 4Å: Chain A: K.24, C.25, N.138, V.139, K.141, E.142, N.143, E.173, H.174 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: S.33, A.34, T.35, L.239, S.240, S.241, Y.242 Ligands: EDO.23 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: T.117, D.293, V.294, L.295 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: R.66, A.121, N.122, K.123, R.283, E.284, N.285, N.286, R.287 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.12 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, I.219, M.224 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: A.116, H.119, T.151, Y.152 Ligands: EDO.10 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.255, G.256, T.257, A.258, G.278, R.279 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: Q.3, V.9, N.235, P.236, I.237, Q.238 Ligands: EDO.17 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Q.28, N.29, P.236, I.237, Q.238, L.239 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: P.12, Y.15, W.231, N.235 Ligands: EDO.15 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: G.39, I.40, M.41, M.42, K.76 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: L.36, M.41, M.42, N.43, K.76 Ligands: EDO.18 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: N.268, D.269, M.270 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: M.20, L.21, E.23, F.230 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: D.32, S.33, A.34, L.239 Ligands: EDO.5 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: K.123, L.163, G.213, E.264 Ligands: CL.26 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: T.103, C.104, N.106, D.107, F.111 Ligand excluded by PLIP

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

MES.2: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

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

01.20: 10 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, G.31, K.137, V.139, S.201, S.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.24, A:L.27 Water bridges: A:S.202 pi-Stacking: A:Y.30, A:Y.30, A:Y.30

1 x SAM: S-ADENOSYLMETHIONINE

SAM.24: 20 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, F.149, K.170 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.43, A:G.71, A:G.81, A:L.100, A:N.101, A:C.115, A:Y.132 Water bridges: A:G.71, A:G.73, A:D.99, A:D.114, A:D.114, A:G.148 Salt bridges: A:D.130

3 x CL: CHLORIDE ION

CL.25: 4 residues within 4Å: Chain A: I.219, D.220, V.223, M.224 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: L.163, L.262, I.282 Ligands: EDO.27 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: I.39, R.79 Ligand excluded by PLIP

2 x ZN: ZINC ION

ZN.29: 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.30: 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

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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