SMTL ID : 4c5l.1 (1 other biounit)

Structure of the pyridoxal kinase from Staphylococcus aureus in complex with pyridoxal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x UEG: 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol(Covalent)

UEG.1: 13 residues within 4Å: Chain A: G.11, S.12, D.13, A.18, G.19, V.42, M.80, V.107, V.109, C.110, K.111, H.210, C.214 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.42 Hydrogen bonds: A:K.111, A:K.111 UEG.4: 12 residues within 4Å: Chain B: G.11, S.12, D.13, A.18, G.19, V.42, M.80, V.107, V.109, C.110, H.210, C.214 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.13, B:V.42 Water bridges: B:M.80

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: K.111, N.139, K.176, G.213 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.139, A:G.213 Water bridges: A:V.109, A:N.139, A:E.142 Salt bridges: A:K.111, A:K.176 SO4.3: 2 residues within 4Å: Chain A: G.72, N.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.72, A:N.98 Salt bridges: A:K.5 SO4.5: 3 residues within 4Å: Chain B: N.139, K.176, G.213 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.139, B:G.213 Water bridges: B:N.139, B:N.139, B:A.212 Salt bridges: B:K.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nodwell, M.B. et al., A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage. J.Am.Chem.Soc. (2014)

Release Date

2014-03-19

Peptides

PHOSPHOMETHYLPYRIMIDINE KINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

PHOSPHOMETHYLPYRIMIDINE KINASE

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