SMTL ID : 9gue.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 57256189

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

19 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: 7 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligands: EDO.16 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: K.24, C.25, V.139, K.141, E.142, N.143, E.173, H.174 Ligand excluded by PLIP EDO.5: 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.6: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: C.154, 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: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.16 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: K.16, M.17, W.190, R.216, E.217, I.219, M.224 Ligand excluded by PLIP EDO.11: 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.12: 5 residues within 4Å: Chain A: Q.3, P.12, Y.15, W.231, N.235 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: M.20, L.21, E.23, F.230 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: M.20, L.21, L.22, Y.222, V.223, A.226 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligands: EDO.3, EDO.9 Ligand excluded by PLIP EDO.17: 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.20: 7 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105 Ligands: EDO.25 Ligand excluded by PLIP EDO.23: 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.24: 5 residues within 4Å: Chain B: T.103, C.104, N.106, D.107, F.111 Ligand excluded by PLIP EDO.25: 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.20 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-[(2~{S})-2-azanyl-4-methyl-pentanoyl]-4-methyl-4,6-bis(oxidanyl)azepan-3-yl]-1,3-dimethyl-purine-2,6-dione

01.14: 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 Hydrophobic interactions: A:D.26, A:Y.30 Hydrogen bonds: A:D.26, 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.18: 21 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:G.81, A:L.100, A:N.101, A:C.115, A:Y.132 Water bridges: A:G.73, A:S.74, A:D.114, A:D.114 Salt bridges: A:D.130

1 x CL: CHLORIDE ION

CL.19: 4 residues within 4Å: Chain A: I.219, D.220, V.223, M.224 Ligand excluded by PLIP

2 x ZN: ZINC ION

ZN.21: 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.22: 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.26: 3 residues within 4Å: Chain B: I.39, R.79, C.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.79 Water bridges: B:R.79, 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

2024-10-02

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

Related Entries With Identical Sequence