› 4yl5

X-ray diffraction
1.7Å resolution

Structure of a putative phosphomethylpyrimidine kinase from Acinetobacter baumannii

Released:
DOI: 10.2210/pdb4yl5/pdb
PDB entry 4yl5 coloured by chain, front view.
PDB entry 4yl5 coloured by chain, side view.
PDB entry 4yl5 coloured by chain, top view.
Source organism: Acinetobacter baumannii IS-123
Entry author: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Function and Biology Details

Reactions catalysed: 
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-2-methyl-5-(phosphomethyl)pyrimidine
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102274 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hydroxylmethylpyrimidine kinase Chain: A
Molecule details ›
Chain: A
Length: 263 amino acids
Theoretical weight: 27.73 KDa
Source organism: Acinetobacter baumannii IS-123
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0J9X285 (Residues: 1-177; Coverage: 100%)
Gene name: ACINIS123_0279
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

1 bound ligand:
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2221
Unit cell:
a: 58.82Å b: 108.1Å c: 88.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.16 0.177
Expression system: Escherichia coli BL21(DE3)

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