› 13pk

X-ray diffraction
2.5Å resolution

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

Released:
DOI: 10.2210/pdb13pk/pdb
PDB entry 13pk coloured by chain, front view.
PDB entry 13pk coloured by chain, side view.
PDB entry 13pk coloured by chain, top view.
Source organism: Trypanosoma brucei
Primary publication:
Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.
Bernstein BE, Michels PA, Hol WG
Nature 385 275-8 (1997)
PMID: 9000079

Function and Biology Details

Reaction catalysed: 
ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139573 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoglycerate kinase, glycosomal Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 415 amino acids
Theoretical weight: 44.7 KDa
Source organism: Trypanosoma brucei
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P07378 (Residues: 5-419; Coverage: 94%)
Sequence domains: Phosphoglycerate kinase
Structure domains: Phosphoglycerate kinase, N-terminal domain

Ligands and Environments

4 bound ligands:
Ligand MG 4 x MG
Ligand PO4 6 x PO4
Ligand ADP 4 x ADP
Ligand 3PG 2 x 3PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P212121
Unit cell:
a: 113.213Å b: 115.959Å c: 171.327Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.221 0.291
Expression system: Escherichia coli BL21

Quick links

Citations

14 review citations

Mechanical processes in biochemistry.
Bustamante et al. (2004)
13 more

8 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
7 more