› 5np8

X-ray diffraction
1.9Å resolution

PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid)

Released:
DOI: 10.2210/pdb5np8/pdb
PDB entry 5np8 coloured by chain, front view.
PDB entry 5np8 coloured by chain, side view.
PDB entry 5np8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation.
Bilsland AE, Liu Y, Turnbull A, Sumpton D, Stevenson K, Cairney CJ, Boyd SM, Roffey J, Jenkinson D, Keith WN
Neoplasia 21 893-907 (2019)
PMID: 31401411

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: 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

3 bound ligands:
Ligand 93T 1 x 93T
Ligand EDO 3 x EDO
Ligand 3PG 1 x 3PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 35.87Å b: 103.9Å c: 50.65Å
α: 90° β: 99.1° γ: 90°
R-values:
R R work R free
0.171 0.168 0.222
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Moving beyond the Tip of the Iceberg: DJ-1 Implications in Cancer Metabolism.
Olivo et al. (2022)
1 other article

2 mentions without citation

Pharmacologically inhibiting phosphoglycerate kinase 1 for glioma with NG52.
Wang et al. (2021)
1 more