- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 2 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.3
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.113, A:T.186
NA.14: 7 residues within 4Å:- Chain B: D.113, T.148, P.149, N.150, E.153, T.186
- Ligands: ATP.15
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.113
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.3: 23 residues within 4Å:- Chain A: D.113, D.118, Y.127, N.150, E.153, T.186, S.187, V.201, I.223, 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, SO4.5, SO4.6
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:Y.127, A:N.150, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226, A:G.234
- Water bridges: A:S.187
ATP.15: 22 residues within 4Å:- Chain B: D.113, D.118, Y.127, N.150, E.153, T.186, S.187, L.199, V.201, I.223, R.224, K.225, V.226, A.228, T.233, G.234, L.263, L.267
- Ligands: MG.13, NA.14, PLP.17, SO4.18
12 PLIP interactions:12 interactions with chain B- Hydrogen bonds: B:Y.127, B:Y.127, B:N.150, B:T.186, B:T.186, B:S.187, B:V.226, B:V.226, B:T.233, B:G.234
- Water bridges: B:T.148, B:F.230
- 2 x PXL: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE(Non-covalent)
PXL.4: 7 residues within 4Å:- Chain A: S.12, H.46, T.47, G.48, V.231, G.232
- Ligands: SO4.5
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.12, A:T.47, A:G.232
- Water bridges: A:T.47
PXL.16: 11 residues within 4Å:- Chain B: S.12, V.19, V.41, F.43, N.45, H.46, T.47, G.48, Y.84, V.231
- Ligands: PLP.17
8 PLIP interactions:8 interactions with chain B- Hydrophobic interactions: B:V.41, B:F.43, B:H.46
- Hydrogen bonds: B:S.12, B:N.45, B:T.47, B:G.48
- Water bridges: B:G.20
- 11 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 7 residues within 4Å:- Chain A: V.231, G.232, T.233, G.234, A.235
- Ligands: ATP.3, PXL.4
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.232, A:T.233, A:T.233, A:G.234, A:A.235
SO4.6: 3 residues within 4Å:- Chain A: L.199
- Ligands: MG.1, ATP.3
2 PLIP interactions:2 interactions with chain A- Water bridges: A:S.187, A:S.187
SO4.7: 4 residues within 4Å:- Chain A: Q.63, R.70, M.93, E.100
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.100
- Salt bridges: A:R.70
SO4.8: 5 residues within 4Å:- Chain A: E.3, E.4, C.5, D.78, H.246
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.4
- Water bridges: A:E.4, A:E.4
- Salt bridges: A:H.246
SO4.9: 3 residues within 4Å:- Chain A: L.31, G.32, K.247
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.247
SO4.10: 4 residues within 4Å:- Chain A: D.145, G.179, D.181
- Ligands: MPD.12
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.181
SO4.11: 4 residues within 4Å:- Chain A: Q.55, V.56, E.61
- Chain B: E.61
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.61
SO4.18: 5 residues within 4Å:- Chain B: D.118, S.187, L.199
- Ligands: MG.13, ATP.15
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:S.187
SO4.19: 5 residues within 4Å:- Chain B: Q.63, Y.66, R.70, D.96, E.100
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.63
- Salt bridges: B:R.70
SO4.20: 5 residues within 4Å:- Chain B: A.144, D.145, G.179, D.181
- Ligands: MPD.24
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.179
SO4.21: 2 residues within 4Å:- Chain B: Q.165, R.220
2 PLIP interactions:2 interactions with chain B- Water bridges: B:Q.165
- Salt bridges: B:R.220
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.12: 4 residues within 4Å:- Chain A: D.181, R.206, R.208
- Ligands: SO4.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.181, A:D.181
MPD.22: 3 residues within 4Å:- Chain B: G.124, M.126, E.130
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.130
MPD.23: 2 residues within 4Å:- Chain B: V.311, L.312
No protein-ligand interaction detected (PLIP)MPD.24: 5 residues within 4Å:- Chain B: D.181, R.206, R.208, V.214
- Ligands: SO4.20
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.214
- Hydrogen bonds: B:D.181, B:R.206
- 1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gandhi, A.K. et al., Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem.Biophys.Res.Commun. (2009)
- Release Date
- 2008-12-23
- Peptides
- Pyridoxal kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x PXL: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE(Non-covalent)
- 11 x SO4: SULFATE ION(Non-functional Binders)
- 4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gandhi, A.K. et al., Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase. Biochem.Biophys.Res.Commun. (2009)
- Release Date
- 2008-12-23
- Peptides
- Pyridoxal kinase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B