- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x PHS: PHOSPHONIC ACID(Non-covalent)
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.2: 12 residues within 4Å:- Chain A: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112
- Ligands: PHS.1
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:K.9, A:Y.49, A:T.91, A:T.91, A:I.109, A:N.112, A:N.112
- Salt bridges: A:K.9, A:R.85, A:R.102
- pi-Stacking: A:F.57, A:F.57
ADP.6: 12 residues within 4Å:- Chain C: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112
- Ligands: PHS.5
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:K.9, C:Y.49, C:T.91, C:T.91, C:I.109, C:N.112, C:N.112
- Salt bridges: C:K.9, C:R.85, C:R.102
- pi-Stacking: C:F.57, C:F.57
ADP.10: 12 residues within 4Å:- Chain E: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112
- Ligands: PHS.9
12 PLIP interactions:12 interactions with chain E- Hydrogen bonds: E:K.9, E:Y.49, E:T.91, E:T.91, E:I.109, E:N.112, E:N.112
- Salt bridges: E:K.9, E:R.85, E:R.102
- pi-Stacking: E:F.57, E:F.57
- 3 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 6 residues within 4Å:- Chain B: R.85, M.88, R.102, H.115, G.116
- Ligands: ATP.4
No protein-ligand interaction detected (PLIP)MG.7: 6 residues within 4Å:- Chain D: R.85, M.88, R.102, H.115, G.116
- Ligands: ATP.8
No protein-ligand interaction detected (PLIP)MG.11: 6 residues within 4Å:- Chain F: R.85, M.88, R.102, H.115, G.116
- Ligands: ATP.12
No protein-ligand interaction detected (PLIP)- 3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.4: 13 residues within 4Å:- Chain B: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116
- Ligands: MG.3
11 PLIP interactions:11 interactions with chain B- Hydrogen bonds: B:K.9, B:K.9, B:R.102, B:N.112, B:G.116
- Salt bridges: B:K.9, B:H.52, B:R.85, B:H.115
- pi-Stacking: B:F.57, B:F.57
ATP.8: 13 residues within 4Å:- Chain D: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116
- Ligands: MG.7
11 PLIP interactions:11 interactions with chain D- Hydrogen bonds: D:K.9, D:K.9, D:R.102, D:N.112, D:G.116
- Salt bridges: D:K.9, D:H.52, D:R.85, D:H.115
- pi-Stacking: D:F.57, D:F.57
ATP.12: 13 residues within 4Å:- Chain F: K.9, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, H.115, G.116
- Ligands: MG.11
11 PLIP interactions:11 interactions with chain F- Hydrogen bonds: F:K.9, F:K.9, F:R.102, F:N.112, F:G.116
- Salt bridges: F:K.9, F:H.52, F:R.85, F:H.115
- pi-Stacking: F:F.57, F:F.57
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Takeishi, S. et al., Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8. To be Published
- Release Date
- 2005-08-23
- Peptides
- nucleotide diphosphate kinase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 3 x PHS: PHOSPHONIC ACID(Non-covalent)
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 3 x MG: MAGNESIUM ION(Non-covalent)
- 3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Takeishi, S. et al., Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8. To be Published
- Release Date
- 2005-08-23
- Peptides
- nucleotide diphosphate kinase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
BE
AF
B