- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-functional Binders)
- 6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)
BEF.2: 8 residues within 4Å:- Chain A: K.16, Y.56, R.92, R.109, H.122, G.123
- Ligands: MG.1, ADP.3
No protein-ligand interaction detected (PLIP)BEF.5: 9 residues within 4Å:- Chain B: K.16, Y.56, R.92, R.109, I.121, H.122, G.123
- Ligands: MG.4, ADP.6
No protein-ligand interaction detected (PLIP)BEF.8: 8 residues within 4Å:- Chain C: K.16, Y.56, R.109, I.121, H.122, G.123
- Ligands: MG.7, ADP.9
No protein-ligand interaction detected (PLIP)BEF.11: 8 residues within 4Å:- Chain D: K.16, Y.56, R.92, R.109, H.122, G.123
- Ligands: MG.10, ADP.12
No protein-ligand interaction detected (PLIP)BEF.14: 9 residues within 4Å:- Chain E: K.16, Y.56, R.92, R.109, I.121, H.122, G.123
- Ligands: MG.13, ADP.15
No protein-ligand interaction detected (PLIP)BEF.17: 8 residues within 4Å:- Chain F: K.16, Y.56, R.109, I.121, H.122, G.123
- Ligands: MG.16, ADP.18
No protein-ligand interaction detected (PLIP)- 6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.3: 12 residues within 4Å:- Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Ligands: MG.1, BEF.2
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:K.16, A:R.109, A:N.119, A:N.119
- Water bridges: A:R.92, A:R.92, A:T.98
- Salt bridges: A:H.59, A:R.92, A:R.109
- pi-Stacking: A:F.64, A:F.64
ADP.6: 13 residues within 4Å:- Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Chain C: E.155
- Ligands: MG.4, BEF.5
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:K.16, B:R.109, B:N.119, B:N.119
- Salt bridges: B:H.59, B:R.92, B:R.109
- pi-Stacking: B:F.64
ADP.9: 12 residues within 4Å:- Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Ligands: MG.7, BEF.8
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:K.16, C:R.109, C:N.119, C:N.119
- Water bridges: C:R.92, C:D.125
- Salt bridges: C:H.59, C:R.92, C:R.109
- pi-Stacking: C:F.64
ADP.12: 12 residues within 4Å:- Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Ligands: MG.10, BEF.11
13 PLIP interactions:13 interactions with chain D- Hydrogen bonds: D:K.16, D:R.109, D:N.119, D:N.119
- Water bridges: D:R.92, D:R.92, D:T.98, D:T.98
- Salt bridges: D:H.59, D:R.92, D:R.109
- pi-Stacking: D:F.64, D:F.64
ADP.15: 13 residues within 4Å:- Chain E: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Chain F: E.155
- Ligands: MG.13, BEF.14
9 PLIP interactions:9 interactions with chain E- Hydrogen bonds: E:K.16, E:T.98, E:R.109, E:N.119, E:N.119
- Salt bridges: E:H.59, E:R.92, E:R.109
- pi-Stacking: E:F.64
ADP.18: 12 residues within 4Å:- Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119
- Ligands: MG.16, BEF.17
9 PLIP interactions:9 interactions with chain F- Hydrogen bonds: F:K.16, F:T.98, F:N.119, F:N.119
- Water bridges: F:R.92
- Salt bridges: F:H.59, F:R.92, F:R.109
- pi-Stacking: F:F.64
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xu, Y.W. et al., AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc.Natl.Acad.Sci.USA (1997)
- Release Date
- 1998-08-12
- Peptides
- NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x MG: MAGNESIUM ION(Non-functional Binders)
- 6 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)
- 6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xu, Y.W. et al., AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc.Natl.Acad.Sci.USA (1997)
- Release Date
- 1998-08-12
- Peptides
- NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
C