SMTL ID : 9emj.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with Toyocamycin and m7GpppA (Cap0-analog)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-1-1-mer

Ligands

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

TO1.1: 16 residues within 4Å: Chain A: G.73, G.75, S.76, D.101, L.102, N.103, G.115, D.116, C.117, D.132, M.133, Y.134, D.135, P.136, F.151 Ligands: GTA.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.75, A:L.102, A:N.103, A:C.117, A:Y.134 Water bridges: A:G.73, A:D.116, A:D.116, A:D.132, A:D.132, A:G.150, A:F.151

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.2: 21 residues within 4Å: Chain A: K.26, C.27, D.28, L.29, Y.32, K.48, Y.134, P.136, T.138, K.139, V.141, K.172, T.174, E.175, H.176, S.177, N.200, S.203, S.204, E.205 Ligands: TO1.1 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:K.26, A:L.29, A:Y.32, A:K.48, A:Y.134, A:K.139, A:K.172, A:T.174, A:H.176, A:S.177, A:N.200, A:S.203, A:S.204, A:S.204 Water bridges: A:D.28, A:D.132, A:D.132, A:D.132, A:D.132, A:H.176, A:N.200, A:N.200, A:S.203 Salt bridges: A:K.139, A:K.139, A:K.139 pi-Stacking: A:Y.32, A:Y.134

1 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.3: 9 residues within 4Å: Chain A: T.58, L.59, T.60, A.190, W.191, C.211, N.212, S.278, K.279 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.60, A:T.60, A:W.191, A:N.212 Water bridges: A:N.15 pi-Stacking: A:W.191, A:W.191

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

EDO.4: 6 residues within 4Å: Chain A: K.40, G.41 Chain B: K.44, E.67, F.69, A.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.44, B:A.105 EDO.7: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.92, B:N.115

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 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 development. To Be Published

Release Date

2024-03-20

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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