- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)
TYD.2: 12 residues within 4Å:- Chain A: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.1, PO4.3
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:Y.63
- Hydrogen bonds: A:K.14, A:Q.94, A:N.114
- Salt bridges: A:H.58, A:R.91, A:R.104
- pi-Stacking: A:Y.63
TYD.5: 12 residues within 4Å:- Chain B: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.4
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:K.14, B:Q.94, B:N.114
- Water bridges: B:K.14, B:H.117
- Salt bridges: B:H.58, B:R.91, B:R.104
- pi-Stacking: B:Y.63
TYD.8: 11 residues within 4Å:- Chain C: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.7
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:Y.63
- Hydrogen bonds: C:K.14, C:K.14, C:N.114
- Salt bridges: C:K.14, C:H.58, C:R.91, C:R.104
- pi-Stacking: C:Y.63
TYD.11: 12 residues within 4Å:- Chain D: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.10, PO4.12
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:Y.63
- Hydrogen bonds: D:K.14, D:Q.94, D:N.114
- Salt bridges: D:H.58, D:R.91, D:R.104
- pi-Stacking: D:Y.63
TYD.14: 12 residues within 4Å:- Chain E: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.13
9 PLIP interactions:9 interactions with chain E- Hydrogen bonds: E:K.14, E:Q.94, E:N.114
- Water bridges: E:K.14, E:Y.55
- Salt bridges: E:H.58, E:R.91, E:R.104
- pi-Stacking: E:Y.63
TYD.17: 11 residues within 4Å:- Chain F: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.16
9 PLIP interactions:9 interactions with chain F- Hydrophobic interactions: F:Y.63
- Hydrogen bonds: F:K.14, F:K.14, F:N.114
- Salt bridges: F:K.14, F:H.58, F:R.91, F:R.104
- pi-Stacking: F:Y.63
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 7 residues within 4Å:- Chain A: G.95, N.96, I.97, R.104, I.111, N.114
- Ligands: TYD.2
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.95, A:I.97, A:D.110, A:N.114
- Salt bridges: A:R.104
PO4.6: 6 residues within 4Å:- Chain B: G.95, N.96, I.97, R.104, I.111, N.114
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:I.97, B:I.111, B:N.114
- Salt bridges: B:R.104
PO4.9: 5 residues within 4Å:- Chain C: G.95, N.96, I.97, R.104, N.114
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:I.97, C:N.114
- Salt bridges: C:R.104
PO4.12: 7 residues within 4Å:- Chain D: G.95, N.96, I.97, R.104, I.111, N.114
- Ligands: TYD.11
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:G.95, D:I.97, D:D.110, D:N.114
- Salt bridges: D:R.104
PO4.15: 6 residues within 4Å:- Chain E: G.95, N.96, I.97, R.104, I.111, N.114
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:I.97, E:I.111, E:N.114
- Salt bridges: E:R.104
PO4.18: 5 residues within 4Å:- Chain F: G.95, N.96, I.97, R.104, N.114
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:I.97, F:N.114
- Salt bridges: F:R.104
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Jeudy, S. et al., Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. J.Virol. (2009)
- Release Date
- 2009-08-11
- Peptides
- Nucleoside diphosphate kinase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
ED
AE
CF
E
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)
- 6 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Jeudy, S. et al., Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. J.Virol. (2009)
- Release Date
- 2009-08-11
- Peptides
- Nucleoside diphosphate kinase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
CC
ED
AE
CF
E