- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 6 x IF9: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate(Non-covalent)
IF9.2: 12 residues within 4Å:- Chain A: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115
- Chain C: E.152
15 PLIP interactions:10 interactions with chain A, 5 interactions with chain C- Hydrophobic interactions: A:T.94, A:V.112
- Water bridges: A:K.12, A:R.88, A:T.94, A:D.121, C:E.152, C:E.152, C:E.152, C:E.152
- Salt bridges: A:R.88
- pi-Stacking: A:F.60, A:F.60
- pi-Cation interactions: A:F.60
- Hydrogen bonds: C:E.152
IF9.4: 13 residues within 4Å:- Chain B: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, D.121
- Chain F: E.152
15 PLIP interactions:12 interactions with chain B, 3 interactions with chain F- Hydrophobic interactions: B:T.94, B:V.112
- Hydrogen bonds: B:R.58, B:R.58, F:E.152
- Water bridges: B:K.12, B:R.88, B:R.88, B:R.88, B:R.88, F:E.152, F:E.152
- Salt bridges: B:R.88
- pi-Stacking: B:F.60, B:F.60
IF9.5: 12 residues within 4Å:- Chain C: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115
- Chain D: E.152
14 PLIP interactions:10 interactions with chain C, 4 interactions with chain D- Hydrophobic interactions: C:V.112
- Hydrogen bonds: C:R.58, C:R.58, D:E.152
- Water bridges: C:R.88, C:R.88, C:T.94, C:T.94, C:T.94, D:E.152, D:E.152, D:E.152
- Salt bridges: C:R.88
- pi-Stacking: C:F.60
IF9.7: 14 residues within 4Å:- Chain A: E.152
- Chain D: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, H.118, D.121
9 PLIP interactions:2 interactions with chain A, 7 interactions with chain D- Hydrogen bonds: A:E.152
- Water bridges: A:E.152, D:Y.52, D:R.88, D:R.88
- Hydrophobic interactions: D:T.94
- Salt bridges: D:R.88
- pi-Stacking: D:F.60, D:F.60
IF9.8: 14 residues within 4Å:- Chain B: E.152
- Chain E: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, H.118, D.121
13 PLIP interactions:11 interactions with chain E, 2 interactions with chain B- Hydrophobic interactions: E:T.94
- Water bridges: E:K.12, E:Y.52, E:Y.52, E:R.88, E:R.88, E:R.114, B:E.152
- Salt bridges: E:R.88
- pi-Stacking: E:F.60, E:F.60
- pi-Cation interactions: E:F.60
- Hydrogen bonds: B:E.152
IF9.9: 13 residues within 4Å:- Chain E: E.152
- Chain F: K.12, Y.52, L.55, R.58, F.60, L.64, R.88, T.94, V.112, G.113, N.115, D.121
15 PLIP interactions:3 interactions with chain E, 12 interactions with chain F- Hydrogen bonds: E:E.152, F:R.58, F:R.58
- Water bridges: E:E.152, E:E.152, F:Y.52, F:R.88, F:R.88, F:R.114, F:D.121
- Hydrophobic interactions: F:T.94
- Salt bridges: F:R.88
- pi-Stacking: F:F.60, F:F.60
- pi-Cation interactions: F:F.60
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shannon, A. et al., An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res. (2024)
- Release Date
- 2023-12-27
- Peptides
- Nucleoside diphosphate kinase B: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.55 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 6 x IF9: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Shannon, A. et al., An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res. (2024)
- Release Date
- 2023-12-27
- Peptides
- Nucleoside diphosphate kinase B: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F