› 5o7d

X-ray diffraction
1.84Å resolution

The X-ray structure of human R38M phosphoglycerate kinase 1 mutant

Released:
DOI: 10.2210/pdb5o7d/pdb
Model geometry
Fit model/data
PDB entry 5o7d coloured by chain, front view.
PDB entry 5o7d coloured by chain, side view.
PDB entry 5o7d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme.
Fiorillo A, Petrosino M, Ilari A, Pasquo A, Cipollone A, Maggi M, Chiaraluce R, Consalvi V
OpenAccess logo PLoS One 13 e0199191 (2018)
PMID: 29995887

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
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: 44.65 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

1 bound ligand:
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 36.05Å b: 106.68Å c: 50.69Å
α: 90° β: 97.32° γ: 90°
R-values:
R R work R free
0.228 0.226 0.267
Expression system: Escherichia coli

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Citations

7 review citations

Metabolic Heterogeneity of Cancer Cells: An Interplay between HIF-1, GLUTs, and AMPK.
Moldogazieva et al. (2020)
6 more

1 mention without citation

In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles.
Alsharif et al. (2020)