SMTL ID : 1rfu.1 (3 other biounits)

Crystal structure of pyridoxal kinase complexed with ADP and PLP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: V.115, Y.127, E.153 Ligands: PLP.2, ADP.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: PLP.2 ZN.4: 4 residues within 4Å: Chain B: D.113, V.115 Ligands: PLP.5, ADP.6 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: PLP.5

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.2: 14 residues within 4Å: Chain A: S.12, V.19, G.20, H.46, T.47, Y.84, Y.127, V.231, G.232, T.233, G.234, D.235 Ligands: ZN.1, ADP.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.84, A:Y.84, A:V.231 Hydrogen bonds: A:S.12, A:T.47, A:Y.127, A:F.230, A:G.232, A:T.233, A:G.234, A:D.235, A:D.235 PLP.5: 14 residues within 4Å: Chain B: S.12, V.19, G.20, H.46, T.47, Y.84, Y.127, V.231, G.232, T.233, G.234, D.235 Ligands: ZN.4, ADP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.19, B:Y.127, B:V.231 Hydrogen bonds: B:S.12, B:T.47, B:Y.127, B:G.232, B:T.233, B:T.233, B:G.234, B:D.235, B:D.235 pi-Stacking: B:Y.84

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 19 residues within 4Å: Chain A: D.118, N.150, T.186, S.187, L.199, M.223, H.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, V.260, M.263, L.267 Ligands: ZN.1, PLP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.118, A:N.150, A:S.187, A:V.226, A:V.226, A:G.234 ADP.6: 18 residues within 4Å: Chain B: D.118, N.150, T.186, S.187, L.199, M.223, H.224, K.225, V.226, A.228, F.230, T.233, G.234, V.260, M.263, L.267 Ligands: ZN.4, PLP.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.118, B:N.150, B:T.186, B:V.226, B:V.226, B:T.233, B:G.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M.-H. et al., Conformational changes in the reaction of pyridoxal kinase. J.BIOL.CHEM. (2004)

Release Date

2004-04-27

Peptides

pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

pyridoxal kinase

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