SMTL ID : 8ov4.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 Ligands: TO1.20 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.7 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.13 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: Y.30, Y.132, K.137, T.172, S.201, S.202, E.203 Ligands: EDO.21 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligands: EDO.3, EDO.10 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: T.117, H.119, D.293, L.295 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.7 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: N.55, T.56, L.57, T.58, K.253, R.255 Ligands: MES.2 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.2 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: D.32, S.33, A.34, L.239 Ligands: EDO.5, EDO.14 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: Q.28, N.29, P.236, I.237, Q.238, L.239 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Q.3, P.12, Y.15, W.231, N.235 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: T.110, L.111, I.112, S.292, V.294 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: M.20, L.21, L.22, Y.222, V.223, A.226 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: W.5, Q.6, P.7, Q.52, S.243, D.246 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: D.114, C.115, A.116, G.148, F.149, T.151, Y.152 Ligands: TO1.20 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: EDO.6 Ligand excluded by PLIP EDO.22: 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.25: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, N.115, T.116, V.117, W.124 Ligands: EDO.26 Ligand excluded by PLIP EDO.26: 10 residues within 4Å: Chain B: C.74, C.75, L.76, Y.77, D.92, L.93, V.109, T.112, L.113 Ligands: EDO.25 Ligand excluded by PLIP

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

MES.2: 8 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 Ligands: EDO.11, EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:T.58, A:W.189

1 x TO1: 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile(Non-covalent)

TO1.20: 16 residues within 4Å: Chain A: G.71, G.73, S.74, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, D.133, F.149 Ligands: EDO.1, EDO.19 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.149 Hydrogen bonds: A:G.73, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:G.71, A:G.73, A:F.149, A:F.149

2 x ZN: ZINC ION(Non-covalent)

ZN.23: 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.24: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kremling, V. et al., SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery. Elife (2024)

Release Date

2023-05-10

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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