- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-hexamer
- Ligands
- 5 x TNM: [(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.2: 1 residues within 4Å:- Ligands: TNM.1
No protein-ligand interaction detected (PLIP)MG.5: 1 residues within 4Å:- Ligands: TNM.4
No protein-ligand interaction detected (PLIP)MG.8: 1 residues within 4Å:- Ligands: TNM.7
No protein-ligand interaction detected (PLIP)MG.11: 2 residues within 4Å:- Chain D: E.58
- Ligands: TNV.10
No protein-ligand interaction detected (PLIP)MG.15: 1 residues within 4Å:- Ligands: TNM.14
No protein-ligand interaction detected (PLIP)MG.17: 1 residues within 4Å:- Ligands: TNM.16
No protein-ligand interaction detected (PLIP)- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 5 residues within 4Å:- Chain A: E.146, K.148
- Chain D: S.74, G.75, P.76
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:K.148, D:S.74
EDO.6: 4 residues within 4Å:- Chain B: V.38, K.148
- Chain E: V.20, A.21
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain E- Hydrogen bonds: B:K.148, E:A.21
- Water bridges: B:K.148, B:N.150
EDO.13: 7 residues within 4Å:- Chain D: V.38, V.147, K.148, P.149, N.150, L.153, Y.154
5 PLIP interactions:5 interactions with chain D- Water bridges: D:N.7, D:V.38, D:V.147, D:K.148, D:N.150
EDO.18: 4 residues within 4Å:- Chain F: G.67, S.70, F.71, S.74
2 PLIP interactions:2 interactions with chain F- Water bridges: F:R.118, F:R.118
EDO.19: 2 residues within 4Å:- Chain F: V.6, N.7
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:N.7
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 5 residues within 4Å:- Chain C: R.92, G.96, V.97, T.98
- Ligands: TNM.7
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:R.92, C:T.98, C:T.98
- Water bridges: C:R.109
GOL.12: 2 residues within 4Å:- Chain D: N.99, L.101
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: D:N.99
- Water bridges: F:G.86
- 1 x TNV: [2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE(Non-covalent)
TNV.10: 14 residues within 4Å:- Chain D: K.16, Y.56, E.58, H.59, F.64, R.92, T.98, R.109, V.116, G.117, N.119, G.123
- Chain F: E.155
- Ligands: MG.11
23 PLIP interactions:22 interactions with chain D, 1 interactions with chain F- Hydrophobic interactions: D:F.64
- Hydrogen bonds: D:K.16, D:N.119, D:G.123, F:E.155
- Water bridges: D:Y.56, D:R.92, D:R.92, D:R.92, D:R.92, D:R.92, D:T.98, D:R.109, D:R.109, D:R.109, D:G.122, D:G.123
- Salt bridges: D:H.59, D:R.92, D:R.92, D:R.109
- pi-Stacking: D:F.64, D:F.64
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Koch, K. et al., Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives. Nucleosides Nucleotides Nucleic Acids (2009)
- Release Date
- 2009-09-29
- Peptides
- Nucleoside diphosphate kinase, cytosolic: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.65 Å
- Oligo State
- homo-hexamer
- Ligands
- 5 x TNM: [(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 1 x TNV: [2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Koch, K. et al., Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives. Nucleosides Nucleotides Nucleic Acids (2009)
- Release Date
- 2009-09-29
- Peptides
- Nucleoside diphosphate kinase, cytosolic: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F