SMTL ID : 1rft.1

Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: Y.127 Ligands: ACP.3 No protein-ligand interaction detected (PLIP) ZN.5: 2 residues within 4Å: Chain B: Y.127 Ligands: ACP.7 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.113, T.148, P.149, T.186 Ligands: ACP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.148 K.6: 5 residues within 4Å: Chain B: D.113, T.148, P.149, T.186 Ligands: ACP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.148

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.3: 16 residues within 4Å: Chain A: Y.127, N.150, T.186, S.187, M.223, H.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.267 Ligands: ZN.1, K.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.150, A:N.150, A:T.186, A:S.187, A:S.187, A:V.226, A:V.226, A:F.230, A:G.232, A:T.233, A:G.234 ACP.7: 16 residues within 4Å: Chain B: Y.127, N.150, T.186, S.187, M.223, H.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.267 Ligands: ZN.5, K.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.127, B:N.150, B:N.150, B:T.186, B:S.187, B:S.187, B:V.226, B:V.226, B:F.230, B:G.232, B:T.233, B:G.234

2 x PXM: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL(Non-covalent)

PXM.4: 8 residues within 4Å: Chain A: S.12, V.19, F.43, H.46, T.47, Y.84, V.231, D.235 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.19, A:F.43 Hydrogen bonds: A:S.12, A:T.47, A:D.235 Water bridges: A:T.47, A:Y.84 PXM.8: 8 residues within 4Å: Chain B: S.12, V.19, F.43, H.46, T.47, Y.84, V.231, D.235 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.19, B:F.43 Hydrogen bonds: B:S.12, B:T.47, B:T.47, B:D.235 Water bridges: B:Y.84

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
A

Pyridoxal kinase

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