› 1ub0

X-ray diffraction
2.05Å resolution

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

Released:
DOI: 10.2210/pdb1ub0/pdb
PDB entry 1ub0 coloured by chain, front view.
PDB entry 1ub0 coloured by chain, side view.
PDB entry 1ub0 coloured by chain, top view.
Source organism: Thermus thermophilus
Entry authors: Bagautdinov B, Kuramitsu S, Yokoyama S, Miyano M, Tahirov TH, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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 domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181931 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Rhodanese domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 26.82 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7SIA0 (Residues: 1-258; Coverage: 100%)
Sequence domains: Phosphomethylpyrimidine kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand DIO 2 x DIO
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: P6522
Unit cell:
a: 105.145Å b: 105.145Å c: 105.469Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.207 0.232
Expression system: Escherichia coli BL21(DE3)

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