› 3c3b

X-ray diffraction
1.8Å resolution

Crystal Structure of human phosphoglycerate kinase bound to D-CDP

Released:
DOI: 10.2210/pdb3c3b/pdb
PDB entry 3c3b coloured by chain, front view.
PDB entry 3c3b coloured by chain, side view.
PDB entry 3c3b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase.
Gondeau C, Chaloin L, Lallemand P, Roy B, Périgaud C, Barman T, Varga A, Vas M, Lionne C, Arold ST
Nucleic Acids Res 36 3620-9 (2008)
PMID: 18463139

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 analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132717 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoglycerate kinase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 420 amino acids
Theoretical weight: 44.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00558 (Residues: 1-417; Coverage: 100%)
Gene names: MIG10, OK/SW-cl.110, PGK1, PGKA
Sequence domains: Phosphoglycerate kinase
Structure domains: Phosphoglycerate kinase, N-terminal domain

Ligands and Environments

2 bound ligands:
Ligand PO4 2 x PO4
Ligand CDP 1 x CDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P1
Unit cell:
a: 35.579Å b: 55.588Å c: 93.805Å
α: 78.92° β: 84.32° γ: 82.95°
R-values:
R R work R free
0.171 0.169 0.241
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Conformational dynamics in phosphoglycerate kinase, an open and shut case?
Bowler MW. (2013)
22 other articles

2 mentions without citation

Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase.
Gondeau et al. (2008)
1 more