- 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: 14 residues within 4Å:- Chain A: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117
- Ligands: MG.1, PO4.3
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:K.14, A:Y.55, A:Q.94, A:N.114, A:H.117
- Salt bridges: A:H.58, A:R.91, A:R.104
- pi-Stacking: A:Y.63
TYD.5: 11 residues within 4Å:- Chain B: K.14, 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- Hydrophobic interactions: B:Y.63
- Hydrogen bonds: B:K.14, B:Y.55, B:R.104, B:N.114
- 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, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117
- Ligands: MG.7
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:Q.94, C:N.114, C:H.117
- Salt bridges: C:H.58, C:R.91, C:R.104
- pi-Stacking: C:Y.63
TYD.11: 14 residues within 4Å:- Chain D: K.14, Y.55, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117
- Ligands: MG.10, PO4.12
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:K.14, D:Y.55, D:Y.55, D:Q.94, D:N.114
- Salt bridges: D:H.58, D:R.91, D:R.104
- pi-Stacking: D:Y.63
TYD.14: 11 residues within 4Å:- Chain E: K.14, H.58, Y.63, L.67, R.91, Q.94, R.104, I.111, G.112, N.114
- Ligands: MG.13
10 PLIP interactions:10 interactions with chain E- Hydrophobic interactions: E:Y.63
- Hydrogen bonds: E:K.14, E:Y.55, E:Y.55, E:R.104, E:N.114
- 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, L.67, R.91, Q.94, R.104, I.111, G.112, N.114, H.117
- Ligands: MG.16
6 PLIP interactions:6 interactions with chain F- Hydrogen bonds: F:Q.94, F:N.114
- Salt bridges: 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: N.96, I.97, R.104, D.110, I.111, N.114
- Ligands: TYD.2
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:I.97, A:N.114
- Salt bridges: A:R.104
PO4.6: 5 residues within 4Å:- Chain B: 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: N.96, I.97, R.104, D.110, I.111, N.114
- Ligands: TYD.11
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:I.97, D:N.114
- Salt bridges: D:R.104
PO4.15: 5 residues within 4Å:- Chain E: 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
BB
DC
FD
BE
DF
F
- 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
BB
DC
FD
BE
DF
F