SMTL ID : 2yxt.2 (1 other biounit)

Human Pyridoxal Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: D.113, T.148, E.153, T.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.148, A:T.186 NA.8: 3 residues within 4Å: Chain B: T.148, E.153, T.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.153 NA.23: 4 residues within 4Å: Chain C: D.113, T.148, E.153, T.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.113 NA.30: 3 residues within 4Å: Chain D: T.148, E.153, T.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.148, D:T.186

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: Q.63, R.70, M.93, I.97, E.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.63 Water bridges: A:E.100 Salt bridges: A:R.70 PO4.9: 6 residues within 4Å: Chain B: C.5, L.31, G.32, F.33, H.246, K.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.31, B:L.31 Salt bridges: B:H.246, B:K.247 PO4.10: 7 residues within 4Å: Chain B: Y.198, D.222, I.223, R.224, H.264, V.306 Ligands: MPD.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.224, B:V.306 Salt bridges: B:H.264 PO4.11: 4 residues within 4Å: Chain B: D.145, G.179, D.181 Ligands: MPD.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.179, B:G.179 Water bridges: B:D.145, B:G.179 PO4.12: 4 residues within 4Å: Chain B: E.155, G.159, R.160, K.161 No protein-ligand interaction detected (PLIP) PO4.13: 6 residues within 4Å: Chain B: Q.63, Y.66, R.70, D.96, I.97, E.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:D.96 Salt bridges: B:R.70 PO4.24: 5 residues within 4Å: Chain C: Q.63, R.70, M.93, I.97, E.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.63 Water bridges: C:D.96 Salt bridges: C:R.70 PO4.31: 6 residues within 4Å: Chain D: C.5, L.31, G.32, F.33, H.246, K.247 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.31, D:L.31 Salt bridges: D:H.246, D:K.247 PO4.32: 7 residues within 4Å: Chain D: Y.198, D.222, I.223, R.224, H.264, V.306 Ligands: MPD.37 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.224, D:V.306 Salt bridges: D:H.264 PO4.33: 4 residues within 4Å: Chain D: D.145, G.179, D.181 Ligands: MPD.38 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.145, D:G.179, D:G.179 Water bridges: D:D.145, D:G.179 PO4.34: 4 residues within 4Å: Chain D: E.155, G.159, R.160, K.161 No protein-ligand interaction detected (PLIP) PO4.35: 6 residues within 4Å: Chain D: Q.63, Y.66, R.70, D.96, I.97, E.100 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.63 Salt bridges: D:R.70

28 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: S.12, V.14, V.19, F.43, T.47, Y.84 Ligand excluded by PLIP MPD.4: 7 residues within 4Å: Chain A: T.186, S.187, I.223, T.233, G.234, F.237, L.263 Ligand excluded by PLIP MPD.5: 6 residues within 4Å: Chain A: R.224, K.225, V.226, H.264, L.267, Q.268 Ligand excluded by PLIP MPD.6: 5 residues within 4Å: Chain A: L.31, G.32, F.33, H.246, K.247 Ligand excluded by PLIP MPD.7: 5 residues within 4Å: Chain A: D.222, I.223, R.224, V.306, V.307 Ligand excluded by PLIP MPD.14: 6 residues within 4Å: Chain B: T.186, L.199, T.233, G.234, F.237 Ligands: MPD.15 Ligand excluded by PLIP MPD.15: 7 residues within 4Å: Chain B: I.223, R.224, H.264, L.267, Q.268 Ligands: PO4.10, MPD.14 Ligand excluded by PLIP MPD.16: 5 residues within 4Å: Chain B: D.181, R.206, R.208, V.214 Ligands: PO4.11 Ligand excluded by PLIP MPD.17: 7 residues within 4Å: Chain B: S.12, V.19, H.46, T.47, V.231 Ligands: MPD.18, MPD.21 Ligand excluded by PLIP MPD.18: 6 residues within 4Å: Chain B: F.43, V.56, Y.84, R.86 Ligands: MPD.17, MPD.21 Ligand excluded by PLIP MPD.19: 3 residues within 4Å: Chain B: M.126, E.130, L.156 Ligand excluded by PLIP MPD.20: 5 residues within 4Å: Chain B: D.173, H.176, S.177, R.206 Chain D: L.312 Ligand excluded by PLIP MPD.21: 5 residues within 4Å: Chain B: T.47, Y.84, Y.127 Ligands: MPD.17, MPD.18 Ligand excluded by PLIP MPD.22: 5 residues within 4Å: Chain B: V.109, I.146, Q.205, T.245, P.249 Ligand excluded by PLIP MPD.25: 6 residues within 4Å: Chain C: S.12, V.14, V.19, F.43, T.47, Y.84 Ligand excluded by PLIP MPD.26: 7 residues within 4Å: Chain C: T.186, S.187, I.223, T.233, G.234, F.237, L.263 Ligand excluded by PLIP MPD.27: 6 residues within 4Å: Chain C: R.224, K.225, V.226, H.264, L.267, Q.268 Ligand excluded by PLIP MPD.28: 5 residues within 4Å: Chain C: L.31, G.32, F.33, H.246, K.247 Ligand excluded by PLIP MPD.29: 5 residues within 4Å: Chain C: D.222, I.223, R.224, V.306, V.307 Ligand excluded by PLIP MPD.36: 6 residues within 4Å: Chain D: T.186, L.199, T.233, G.234, F.237 Ligands: MPD.37 Ligand excluded by PLIP MPD.37: 7 residues within 4Å: Chain D: I.223, R.224, H.264, L.267, Q.268 Ligands: PO4.32, MPD.36 Ligand excluded by PLIP MPD.38: 5 residues within 4Å: Chain D: D.181, R.206, R.208, V.214 Ligands: PO4.33 Ligand excluded by PLIP MPD.39: 7 residues within 4Å: Chain D: S.12, V.19, H.46, T.47, V.231 Ligands: MPD.40, MPD.43 Ligand excluded by PLIP MPD.40: 6 residues within 4Å: Chain D: F.43, V.56, Y.84, R.86 Ligands: MPD.39, MPD.43 Ligand excluded by PLIP MPD.41: 3 residues within 4Å: Chain D: M.126, E.130, L.156 Ligand excluded by PLIP MPD.42: 5 residues within 4Å: Chain B: L.312 Chain D: D.173, H.176, S.177, R.206 Ligand excluded by PLIP MPD.43: 5 residues within 4Å: Chain D: T.47, Y.84, Y.127 Ligands: MPD.39, MPD.40 Ligand excluded by PLIP MPD.44: 5 residues within 4Å: Chain D: V.109, I.146, Q.205, T.245, P.249 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Musayev, F.N. et al., Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Protein Sci. (2007)

Release Date

2008-03-11

Peptides

Pyridoxal kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyridoxal kinase

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