- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x TEP: THEOPHYLLINE(Non-covalent)
TEP.2: 6 residues within 4Å:- Chain A: S.12, G.20, T.47, V.231, D.235
- Ligands: MPD.3
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.12, A:G.20
- Water bridges: A:Y.84, A:D.235
TEP.12: 7 residues within 4Å:- Chain B: S.12, H.46, T.47, Y.84, V.231, D.235
- Ligands: MPD.13
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.12, B:T.47
- Water bridges: B:Y.84
- 14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.3: 8 residues within 4Å:- Chain A: S.12, V.14, V.19, G.20, F.43, H.46, T.47
- Ligands: TEP.2
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:V.14, A:F.43, A:T.47
- Hydrogen bonds: A:T.47
MPD.4: 6 residues within 4Å:- Chain A: T.186, I.223, T.233, G.234, F.237, L.263
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.223, A:F.237
- Hydrogen bonds: A:T.233
MPD.5: 4 residues within 4Å:- Chain A: K.76, Y.77, D.78, N.105
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:K.76, A:N.105
- Hydrogen bonds: A:K.76, A:N.105
- Water bridges: A:N.105, A:R.107
MPD.6: 6 residues within 4Å:- Chain A: I.223, R.224, K.225, V.226, H.264, I.271
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:I.223, A:V.226
MPD.7: 4 residues within 4Å:- Chain A: C.5, L.31, G.32, K.247
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.247
MPD.13: 7 residues within 4Å:- Chain B: S.12, V.19, H.46, T.47, Y.84
- Ligands: TEP.12, MPD.17
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:H.46, B:Y.84, B:Y.84
- Hydrogen bonds: B:T.47
MPD.14: 4 residues within 4Å:- Chain B: D.181, R.206, R.207, R.208
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.181, B:R.208
MPD.15: 3 residues within 4Å:- Chain B: P.191, P.193, R.220
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:P.193
- Water bridges: B:R.220
MPD.16: 3 residues within 4Å:- Chain B: M.126, E.130, L.156
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.156
- Hydrogen bonds: B:E.130
- Water bridges: B:M.126
MPD.17: 5 residues within 4Å:- Chain B: F.43, W.52, Y.84, R.86
- Ligands: MPD.13
No protein-ligand interaction detected (PLIP)MPD.18: 5 residues within 4Å:- Chain B: T.186, L.199, T.233, F.237
- Ligands: MPD.20
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:F.237
- Water bridges: B:T.186
MPD.19: 4 residues within 4Å:- Chain B: V.109, Q.205, T.245, P.249
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:V.109, B:P.249
- Hydrogen bonds: B:T.245
- Water bridges: B:Y.79
MPD.20: 7 residues within 4Å:- Chain B: I.223, R.224, V.226, H.264, L.267
- Ligands: MPD.18, MPD.21
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:H.264, B:L.267
- Hydrogen bonds: B:H.264
MPD.21: 8 residues within 4Å:- Chain B: Y.198, D.222, I.223, R.224, H.264, V.306, V.307
- Ligands: MPD.20
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:Y.198, B:R.224, B:V.307
- Hydrogen bonds: B:R.224, B:H.264
- 7 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 2 residues within 4Å:- Chain A: L.156, K.161
No protein-ligand interaction detected (PLIP)SO4.9: 6 residues within 4Å:- Chain A: Q.63, R.70, M.93, D.96, I.97, E.100
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.100
- Salt bridges: A:R.70
SO4.10: 7 residues within 4Å:- Chain A: S.40, V.56, L.57, T.85, R.86, D.87, F.90
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.40, A:S.40, A:R.86, A:D.87
SO4.22: 5 residues within 4Å:- Chain B: Q.63, Y.66, M.93, D.96, E.100
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Q.63
- Water bridges: B:D.96, B:D.96
SO4.23: 4 residues within 4Å:- Chain B: E.4, C.5, D.78, H.246
4 PLIP interactions:4 interactions with chain B- Water bridges: B:E.4, B:D.78, B:D.78
- Salt bridges: B:H.246
SO4.24: 6 residues within 4Å:- Chain B: C.5, L.31, G.32, F.33, H.246, K.247
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:C.5
- Salt bridges: B:H.246, B:K.247
SO4.25: 4 residues within 4Å:- Chain B: E.155, L.156, G.159, R.160
No protein-ligand interaction detected (PLIP)- 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 2.10 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x TEP: THEOPHYLLINE(Non-covalent)
- 14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 7 x SO4: SULFATE ION(Non-functional Binders)
- 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