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

Human Pyridoxal Kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.118, S.187 Ligands: ATP.5, MPD.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain B: D.118, S.187 Ligands: ATP.14, MPD.22 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.118, H2O.9, H2O.9 MG.24: 4 residues within 4Å: Chain C: D.118, S.187 Ligands: ATP.28, MPD.31 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.118, H2O.19, H2O.19 MG.32: 4 residues within 4Å: Chain D: D.118, S.187 Ligands: ATP.37, MPD.45 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.118, H2O.27, H2O.27

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

NA.2: 6 residues within 4Å: Chain A: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.113, A:T.186 NA.10: 6 residues within 4Å: Chain B: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.113, B:T.148 NA.25: 6 residues within 4Å: Chain C: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.113 NA.33: 6 residues within 4Å: Chain D: D.113, T.148, P.149, N.150, T.186 Ligands: ATP.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.148, D:T.186

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

PO4.3: 5 residues within 4Å: Chain A: C.5, L.31, G.32, H.246, K.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.32 Water bridges: A:C.5 Salt bridges: A:K.247 PO4.4: 1 residues within 4Å: Chain A: G.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.159 PO4.11: 4 residues within 4Å: Chain B: E.155, L.156, R.160, K.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.155 PO4.12: 5 residues within 4Å: Chain B: C.5, L.31, G.32, F.33, H.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.31 Salt bridges: B:H.246 PO4.13: 4 residues within 4Å: Chain B: Q.63, Y.66, D.96, E.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.63 PO4.26: 5 residues within 4Å: Chain C: C.5, L.31, G.32, H.246, K.247 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.32 Water bridges: C:C.5 Salt bridges: C:K.247 PO4.27: 1 residues within 4Å: Chain C: G.159 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.159 PO4.34: 4 residues within 4Å: Chain D: E.155, L.156, R.160, K.161 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.155 PO4.35: 5 residues within 4Å: Chain D: C.5, L.31, G.32, F.33, H.246 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.31 Salt bridges: D:H.246 PO4.36: 4 residues within 4Å: Chain D: Q.63, Y.66, D.96, E.100 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.63

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 24 residues within 4Å: Chain A: D.113, V.115, D.118, Y.127, T.148, 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.1, NA.2, MPD.8 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.153, A:E.153, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226, A:T.233, A:G.234 Water bridges: A:D.235 ATP.14: 21 residues within 4Å: Chain B: D.113, D.118, Y.127, T.148, N.150, E.153, T.186, S.187, L.199, V.201, R.224, K.225, V.226, A.228, T.233, G.234, L.263, L.267 Ligands: MG.9, NA.10, MPD.22 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Y.127, B:N.150, B:E.153, 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, B:T.233, B:D.235 ATP.28: 24 residues within 4Å: Chain C: D.113, V.115, D.118, Y.127, T.148, 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.24, NA.25, MPD.31 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Y.127, C:E.153, C:E.153, C:T.186, C:T.186, C:S.187, C:V.226, C:V.226, C:T.233, C:G.234 Water bridges: C:D.118, C:D.118, C:T.148, C:D.235 ATP.37: 21 residues within 4Å: Chain D: D.113, D.118, Y.127, T.148, N.150, E.153, T.186, S.187, L.199, V.201, R.224, K.225, V.226, A.228, T.233, G.234, L.263, L.267 Ligands: MG.32, NA.33, MPD.45 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.150, D:E.153, D:T.186, D:T.186, D:S.187, D:V.226, D:V.226, D:T.233 Water bridges: D:F.230, D:T.233, D:D.235

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

MPD.6: 7 residues within 4Å: Chain A: Q.63, Y.66, R.70, M.93, D.96, I.97, E.100 Ligand excluded by PLIP MPD.7: 6 residues within 4Å: Chain A: S.12, V.19, F.43, H.46, T.47, Y.84 Ligand excluded by PLIP MPD.8: 3 residues within 4Å: Chain A: D.118 Ligands: MG.1, ATP.5 Ligand excluded by PLIP MPD.15: 8 residues within 4Å: Chain B: K.102, P.142, A.144, D.145, G.179, P.180, D.181 Ligands: MPD.17 Ligand excluded by PLIP MPD.16: 9 residues within 4Å: Chain B: S.12, V.19, G.20, H.46, T.47, Y.84, V.231, D.235 Ligands: MPD.21 Ligand excluded by PLIP MPD.17: 5 residues within 4Å: Chain B: D.181, R.206, R.207, R.208 Ligands: MPD.15 Ligand excluded by PLIP MPD.18: 4 residues within 4Å: Chain B: L.312 Chain D: D.173, S.177, R.206 Ligand excluded by PLIP MPD.19: 4 residues within 4Å: Chain B: H.248, P.249, N.250, N.251 Ligand excluded by PLIP MPD.20: 3 residues within 4Å: Chain B: E.123, G.124, E.130 Ligand excluded by PLIP MPD.21: 6 residues within 4Å: Chain B: F.43, W.52, V.56, Y.84, R.86 Ligands: MPD.16 Ligand excluded by PLIP MPD.22: 4 residues within 4Å: Chain B: D.118, L.199 Ligands: MG.9, ATP.14 Ligand excluded by PLIP MPD.23: 1 residues within 4Å: Chain B: P.191 Ligand excluded by PLIP MPD.29: 7 residues within 4Å: Chain C: Q.63, Y.66, R.70, M.93, D.96, I.97, E.100 Ligand excluded by PLIP MPD.30: 6 residues within 4Å: Chain C: S.12, V.19, F.43, H.46, T.47, Y.84 Ligand excluded by PLIP MPD.31: 3 residues within 4Å: Chain C: D.118 Ligands: MG.24, ATP.28 Ligand excluded by PLIP MPD.38: 8 residues within 4Å: Chain D: K.102, P.142, A.144, D.145, G.179, P.180, D.181 Ligands: MPD.40 Ligand excluded by PLIP MPD.39: 9 residues within 4Å: Chain D: S.12, V.19, G.20, H.46, T.47, Y.84, V.231, D.235 Ligands: MPD.44 Ligand excluded by PLIP MPD.40: 5 residues within 4Å: Chain D: D.181, R.206, R.207, R.208 Ligands: MPD.38 Ligand excluded by PLIP MPD.41: 4 residues within 4Å: Chain B: D.173, S.177, R.206 Chain D: L.312 Ligand excluded by PLIP MPD.42: 4 residues within 4Å: Chain D: H.248, P.249, N.250, N.251 Ligand excluded by PLIP MPD.43: 3 residues within 4Å: Chain D: E.123, G.124, E.130 Ligand excluded by PLIP MPD.44: 6 residues within 4Å: Chain D: F.43, W.52, V.56, Y.84, R.86 Ligands: MPD.39 Ligand excluded by PLIP MPD.45: 4 residues within 4Å: Chain D: D.118, L.199 Ligands: MG.32, ATP.37 Ligand excluded by PLIP MPD.46: 1 residues within 4Å: Chain D: P.191 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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