SMTL ID : 5b6a.1

Structure of Pyridoxal Kinasefrom Pseudomonas Aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 6 residues within 4Å: Chain A: S.12, A.19, F.43, H.46, T.47, Y.85 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.12, A:T.47, A:T.47 Water bridges: A:S.12, A:G.20, A:T.47, A:T.47, A:Y.85, A:D.225, A:D.225 TRS.4: 6 residues within 4Å: Chain B: S.12, A.19, F.43, H.46, T.47, Y.85 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.12, B:T.47, B:T.47 Water bridges: B:S.12, B:G.20, B:Y.85, B:D.225, B:D.225

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: V.116, D.225 Ligands: PO4.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.225, H2O.2 MG.5: 3 residues within 4Å: Chain B: V.116, D.225 Ligands: PO4.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.225, H2O.5

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

PO4.3: 4 residues within 4Å: Chain A: N.148, V.223, G.224 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.148, A:G.224 Water bridges: A:K.184, A:G.222, A:G.222, A:G.222, A:V.223, A:D.225 Salt bridges: A:K.184 PO4.6: 4 residues within 4Å: Chain B: N.148, V.223, G.224 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.148, B:G.224 Water bridges: B:K.184, B:G.222, B:G.222, B:G.222, B:V.223, B:D.225 Salt bridges: B:K.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M.I. et al., Crystal structure and catalytic mechanism of pyridoxal kinase from Pseudomonas aeruginosa. Biochem.Biophys.Res.Commun. (2016)

Release Date

2016-08-10

Peptides

Pyridoxal kinase PdxY: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyridoxal kinase PdxY