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

Human Pyridoxal Kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 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

2 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:T.186, 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

5 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

2 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

12 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.66, A:D.96, A:I.97, A:E.100 Hydrogen bonds: A:Q.63, A:R.70 MPD.7: 6 residues within 4Å: Chain A: S.12, V.19, F.43, H.46, T.47, Y.84 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.43, A:H.46, A:T.47 Hydrogen bonds: A:S.12 MPD.8: 3 residues within 4Å: Chain A: D.118 Ligands: MG.1, ATP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:S.187 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.144, B:G.179 Water bridges: B:D.181, B:D.181 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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.47, B:Y.84 Hydrogen bonds: B:T.47, B:T.47 MPD.17: 5 residues within 4Å: Chain B: D.181, R.206, R.207, R.208 Ligands: MPD.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.181, B:R.206 MPD.18: 1 residues within 4Å: Chain B: L.312 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.312 MPD.19: 4 residues within 4Å: Chain B: H.248, P.249, N.250, N.251 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.250, B:N.251 Hydrogen bonds: B:H.248, B:N.250, B:N.251 MPD.20: 3 residues within 4Å: Chain B: E.123, G.124, E.130 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.130, B:E.130 Water bridges: B:M.126 MPD.21: 6 residues within 4Å: Chain B: F.43, W.52, V.56, Y.84, R.86 Ligands: MPD.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.43, B:W.52, B:Y.84 Hydrogen bonds: B:R.86 MPD.22: 4 residues within 4Å: Chain B: D.118, L.199 Ligands: MG.9, ATP.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.199 Water bridges: B:D.118, B:S.187, B:S.188 MPD.23: 1 residues within 4Å: Chain B: P.191 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.165

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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