› 6e8y

X-ray diffraction
1.85Å resolution

Unliganded Human Glycerol 3-Phosphate Dehydrogenase

Released:
DOI: 10.2210/pdb6e8y/pdb
PDB entry 6e8y coloured by chain, front view.
PDB entry 6e8y coloured by chain, side view.
PDB entry 6e8y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.
Mydy LS, Cristobal JR, Katigbak RD, Bauer P, Reyes AC, Kamerlin SCL, Richard JP, Gulick AM
Biochemistry 58 1061-1073 (2019)
PMID: 30640445

Function and Biology Details

Reaction catalysed: 
sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149368 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic Chains: A, B
Molecule details ›
Chains: A, B
Length: 349 amino acids
Theoretical weight: 37.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P21695 (Residues: 1-349; Coverage: 100%)
Gene name: GPD1
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand PO4 1 x PO4
Ligand 3SY 1 x 3SY
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 63.37Å b: 76.16Å c: 64.39Å
α: 90° β: 96.03° γ: 90°
R-values:
R R work R free
0.172 0.17 0.21
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Linear Free Energy Relationships for Enzymatic Reactions: Fresh Insight from a Venerable Probe.
Richard et al. (2021)
10 other articles

3 mentions without citation

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies.
Mydy et al. (2019)
2 more