- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
NA.2: 7 residues within 4Å:- Chain A: D.113, T.148, P.149, N.150, E.153, T.186
- Ligands: ATP.4
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.113, A:T.186
NA.12: 7 residues within 4Å:- Chain B: D.113, T.148, P.149, N.150, E.153, T.186
- Ligands: ATP.14
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.113, B:T.148
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.4: 23 residues within 4Å:- Chain A: D.113, D.118, Y.127, N.150, E.153, T.186, S.187, V.201, R.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.263, L.267
- Ligands: MG.1, NA.2, MG.3, MPD.6, GT1.10
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:N.150, A:E.153, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226
- Water bridges: A:E.153
ATP.14: 24 residues within 4Å:- Chain B: D.113, V.115, D.118, N.150, E.153, T.186, S.187, L.199, V.201, R.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.263, L.267
- Ligands: MG.11, NA.12, MG.13, GT1.15, MPD.17
11 PLIP interactions:11 interactions with chain B- Hydrogen bonds: B:N.150, B:T.186, B:T.186, B:S.187, B:V.226, B:V.226, B:T.233
- Water bridges: B:T.148, B:E.153, B:F.230, B:T.233
- 2 x GT0: 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol(Non-covalent)
GT0.5: 9 residues within 4Å:- Chain A: S.12, G.20, H.46, T.47, Y.84, V.231, D.235
- Ligands: MG.3, GT1.10
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:T.47
- Hydrogen bonds: A:S.12, A:G.20, A:T.47, A:T.47, A:D.235
- Water bridges: A:Y.84, A:Y.84
GT0.24: 10 residues within 4Å:- Chain B: S.12, V.19, G.20, F.43, H.46, T.47, V.231, D.235
- Ligands: MG.13, GT1.15
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:V.19, B:F.43
- Hydrogen bonds: B:S.12, B:G.20, B:T.47, B:D.235
- Water bridges: B:Y.84
- 6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.6: 5 residues within 4Å:- Chain A: D.118, W.120, L.199
- Ligands: MG.1, ATP.4
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:W.120, A:L.199
- Water bridges: A:K.119
MPD.16: 6 residues within 4Å:- Chain B: D.181, R.206, R.207, R.208, V.214
- Ligands: MPD.20
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.214
- Hydrogen bonds: B:D.181, B:R.206
MPD.17: 4 residues within 4Å:- Chain B: D.118, W.120
- Ligands: MG.11, ATP.14
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:W.120
- Hydrogen bonds: B:D.118
- Water bridges: B:S.187
MPD.18: 1 residues within 4Å:- Chain B: L.312
No protein-ligand interaction detected (PLIP)MPD.19: 3 residues within 4Å:- Chain B: Q.165, P.191, P.193
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:P.191, B:P.193
- Water bridges: B:Q.165
MPD.20: 5 residues within 4Å:- Chain B: A.144, D.145, G.179, D.181
- Ligands: MPD.16
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.181
- Water bridges: B:A.144
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.7: 4 residues within 4Å:- Chain A: Q.63, R.70, M.93, E.100
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.70, A:R.70, A:E.100
SO4.8: 4 residues within 4Å:- Chain A: E.155, G.159, R.160, K.161
No protein-ligand interaction detected (PLIP)SO4.9: 6 residues within 4Å:- Chain A: C.5, L.31, G.32, F.33, H.246, K.247
1 PLIP interactions:1 interactions with chain A- Water bridges: A:E.34
SO4.21: 2 residues within 4Å:- Chain B: E.155, G.159
No protein-ligand interaction detected (PLIP)SO4.22: 4 residues within 4Å:- Chain B: Q.63, R.70, D.96, E.100
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:R.70
SO4.23: 4 residues within 4Å:- Chain B: L.31, G.32, F.33, K.247
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:C.5
- Salt bridges: B:K.247
- 2 x GT1: [5-hydroxy-4-(methoxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)
GT1.10: 12 residues within 4Å:- Chain A: S.12, G.20, T.47, Y.84, V.231, G.232, T.233, G.234, D.235
- Ligands: MG.3, ATP.4, GT0.5
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:Y.84, A:V.231
- Hydrogen bonds: A:G.20, A:T.47, A:G.232, A:T.233, A:G.234, A:D.235
- Water bridges: A:Y.84, A:Y.84, A:Y.127, A:Y.127
GT1.15: 13 residues within 4Å:- Chain B: S.12, V.19, G.20, T.47, Y.84, V.231, G.232, T.233, G.234, D.235
- Ligands: MG.13, ATP.14, GT0.24
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:Y.84, B:V.231
- Hydrogen bonds: B:G.20, B:T.47, B:G.232, B:G.232, B:T.233, B:T.233, B:G.234, B:D.235
- Water bridges: B:Y.84
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gandhi, A.K. et al., Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition. Plos One (2012)
- Release Date
- 2012-05-02
- Peptides
- Pyridoxal kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x GT0: 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol(Non-covalent)
- 6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 2 x GT1: [5-hydroxy-4-(methoxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gandhi, A.K. et al., Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition. Plos One (2012)
- Release Date
- 2012-05-02
- Peptides
- Pyridoxal kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B