- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.30 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
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.113, A:T.186
- Water bridges: A:T.148
NA.12: 7 residues within 4Å:- Chain B: D.113, T.148, P.149, N.150, E.153, T.186
- Ligands: ATP.13
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.3: 22 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, SO4.7, SO4.8
12 PLIP interactions:12 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:Y.127, A:Y.127, A:T.233, A:T.233
ATP.13: 24 residues within 4Å:- Chain B: D.113, G.117, 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, F.237, L.263, L.267
- Ligands: MG.11, NA.12, SO4.19, SO4.20
11 PLIP interactions:11 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
- Water bridges: B:T.148, B:F.230
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 5 residues within 4Å:- Chain A: C.5, L.31, G.32, F.33, K.247
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:C.5
- Salt bridges: A:H.246, A:K.247
SO4.5: 4 residues within 4Å:- Chain A: E.155, L.156, G.159, K.161
No protein-ligand interaction detected (PLIP)SO4.6: 5 residues within 4Å:- Chain A: A.144, D.145, G.179, D.181
- Ligands: MPD.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.181
SO4.7: 3 residues within 4Å:- Chain A: D.118
- Ligands: MG.1, ATP.3
2 PLIP interactions:2 interactions with chain A- Water bridges: A:S.187, A:S.187
SO4.8: 6 residues within 4Å:- Chain A: V.231, G.232, T.233, G.234, N.235
- Ligands: ATP.3
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.232, A:G.234, A:N.235, A:N.235
- Water bridges: A:T.233
SO4.14: 3 residues within 4Å:- Chain B: E.155, R.160, K.161
No protein-ligand interaction detected (PLIP)SO4.15: 4 residues within 4Å:- Chain B: C.5, L.31, G.32, H.246
2 PLIP interactions:2 interactions with chain B- Water bridges: B:E.34
- Salt bridges: B:H.246
SO4.16: 5 residues within 4Å:- Chain A: V.56, E.61
- Chain B: Q.55, V.56, E.61
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.61
- Water bridges: A:Q.55
SO4.17: 2 residues within 4Å:- Chain B: R.70, E.100
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.63
- Salt bridges: B:R.70
SO4.18: 4 residues within 4Å:- Chain B: P.142, D.145, G.179, D.181
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.145
- Water bridges: B:G.179
SO4.19: 5 residues within 4Å:- Chain B: D.118, S.187, L.199
- Ligands: MG.11, ATP.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.118, B:S.187
SO4.20: 7 residues within 4Å:- Chain B: V.231, G.232, T.233, G.234, N.235
- Ligands: ATP.13, MPD.25
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:G.232, B:T.233, B:T.233, B:G.234, B:N.235, B:N.235
- 8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.9: 4 residues within 4Å:- Chain A: D.181, R.206, R.208
- Ligands: SO4.6
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:R.206, A:R.208
- Hydrogen bonds: A:D.181
MPD.10: 6 residues within 4Å:- Chain A: Q.63, Y.66, R.70, M.93, D.96, E.100
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:Y.66, A:D.96, A:E.100
- Hydrogen bonds: A:Q.63, A:R.70
MPD.21: 5 residues within 4Å:- Chain B: D.181, R.206, R.207, R.208, V.214
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:V.214
- Hydrogen bonds: B:D.181, B:R.206
MPD.22: 2 residues within 4Å:- Chain B: V.311, L.312
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:L.312
MPD.23: 4 residues within 4Å:- Chain B: H.248, P.249, N.250, N.251
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:P.249, B:N.250
- Hydrogen bonds: B:N.250, B:N.251
MPD.24: 3 residues within 4Å:- Chain B: G.124, E.130, F.152
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:F.152
- Hydrogen bonds: B:E.130, B:E.130
MPD.25: 9 residues within 4Å:- Chain B: S.12, V.19, F.43, H.46, T.47, Y.84, V.231, N.235
- Ligands: SO4.20
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:V.19, B:F.43, B:Y.84, B:V.231
- Hydrogen bonds: B:G.20, B:T.47, B:T.47, B:N.235
- Water bridges: B:Y.84, B:N.235
MPD.26: 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:Q.165
- 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 2.30 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)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 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