› 6m61

X-ray diffraction
1.82Å resolution

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) with inhibitor heptelidic acid

Released:
DOI: 10.2210/pdb6m61/pdb
PDB entry 6m61 coloured by chain, front view.
PDB entry 6m61 coloured by chain, side view.
PDB entry 6m61 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Biosynthesis of the fungal glyceraldehyde-3-phosphate dehydrogenase inhibitor heptelidic acid and mechanism of self-resistance
Yan Y, Zang X, Cooper SJ, Lin H, Zhou J, Tang Y
Chem Sci 11 9554-9562 (2020)

Function and Biology Details

Reaction catalysed: 
D-glyceraldehyde 3-phosphate + phosphate + NAD(+) = 3-phospho-D-glyceroyl phosphate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137626 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyceraldehyde-3-phosphate dehydrogenase Chains: O, P, Q, R
Molecule details ›
Chains: O, P, Q, R
Length: 336 amino acids
Theoretical weight: 36.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04406 (Residues: 1-335; Coverage: 100%)
Gene names: CDABP0047, GAPD, GAPDH, OK/SW-cl.12
Sequence domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
5 bound ligands:
Ligand EDO 11 x EDO
Ligand PEG 1 x PEG
Ligand ZN 5 x ZN
Ligand F4F 2 x F4F
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 81.358Å b: 135.078Å c: 146.227Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links