› 2wzd

X-ray diffraction
1.56Å resolution

The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with ADP, 3PG and aluminium trifluoride

Released:
DOI: 10.2210/pdb2wzd/pdb
PDB entry 2wzd coloured by chain, front view.
PDB entry 2wzd coloured by chain, side view.
PDB entry 2wzd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis.
Cliff MJ, Bowler MW, Varga A, Marston JP, Szabó J, Hounslow AM, Baxter NJ, Blackburn GM, Vas M, Waltho JP
J Am Chem Soc 132 6507-16 (2010)
PMID: 20397725

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 Chain: A
Molecule details ›
Chain: A
Length: 417 amino acids
Theoretical weight: 44.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
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

5 bound ligands:
Ligand MG 1 x MG
Ligand CL 1 x CL
Ligand AF3 1 x AF3
Ligand ADP 1 x ADP
Ligand 3PG 1 x 3PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 39.38Å b: 91.59Å c: 108.48Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.166 0.202
Expression system: Escherichia coli BL21

Quick links

Citations

7 review citations

A structural perspective of compensatory evolution.
Ivankov et al. (2014)
6 more

1 mention without citation

A potent PGK1 antagonist reveals PGK1 regulates the production of IL-1β and IL-6.
Liao et al. (2022)