› 5m3u

X-ray diffraction
1.81Å resolution

The X-ray structure of human V216F phosphoglycerate kinase 1 mutant

Released:
DOI: 10.2210/pdb5m3u/pdb
PDB entry 5m3u coloured by chain, front view.
PDB entry 5m3u coloured by chain, side view.
PDB entry 5m3u 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
PLoS One 13 e0199191 (2018)
PMID: 29995887

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: 416 amino acids
Theoretical weight: 44.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00558 (Residues: 2-417; 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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-3
Spacegroup: P21
Unit cell:
a: 35.65Å b: 106.031Å c: 50.097Å
α: 90° β: 98.71° γ: 90°
R-values:
R R work R free
0.194 0.192 0.242
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