› 8yt5

X-ray diffraction
1.6Å resolution

SP1746 treated with EDTA, in complex with ADP

Released:
DOI: 10.2210/pdb8yt5/pdb
PDB entry 8yt5 coloured by chain, front view.
PDB entry 8yt5 coloured by chain, side view.
PDB entry 8yt5 coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Structural and biochemical characterization of a nucleotide hydrolase from Streptococcus pneumonia.
Jin Y, Ke J, Zheng P, Zhang H, Zhu Z, Niu L
Structure (2024)
PMID: 38701795

Function and Biology Details

Reaction catalysed: 
P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H(2)O = 2 ADP
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243913 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
bis(5'-nucleosyl)-tetraphosphatase (symmetrical) Chain: A
Molecule details ›
Chain: A
Length: 216 amino acids
Theoretical weight: 25.05 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A0H2URF8 (Residues: 1-197; Coverage: 100%)
Gene name: SP_1746
Sequence domains: HD domain

Ligands and Environments

2 bound ligands:
Ligand ADP 1 x ADP
Ligand FE 2 x FE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P3221
Unit cell:
a: 69.271Å b: 69.271Å c: 88.463Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.194 0.202
Expression system: Escherichia coli

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