› 8xw7

X-ray diffraction
2.1Å resolution

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and ADP

Released:
DOI: 10.2210/pdb8xw7/pdb
PDB entry 8xw7 coloured by chain, front view.
PDB entry 8xw7 coloured by chain, side view.
PDB entry 8xw7 coloured by chain, top view.
Source organism: Streptococcus pneumoniae R6
Primary publication:
Structural basis of nucleotide selectivity in pyruvate kinase.
Taguchi A, Nakashima R, Nishino K
J Mol Biol 168708 (2024)
PMID: 39009072

Function and Biology Details

Reaction catalysed: 
ATP + pyruvate = ADP + phosphoenolpyruvate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-218328 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyruvate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 521 amino acids
Theoretical weight: 56.99 KDa
Source organism: Streptococcus pneumoniae R6
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8DQ84 (Residues: 1-501; Coverage: 100%)
Gene names: pykF, spr0797
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand MG 4 x MG
Ligand K 2 x K
Ligand FBP 2 x FBP
Ligand OXL 2 x OXL
Ligand ADP 2 x ADP
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2221
Unit cell:
a: 123.184Å b: 255.539Å c: 88.133Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.227
Expression system: Escherichia coli

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