› 1ml3

X-ray diffraction
2.5Å resolution

Evidences for a flip-flop catalytic mechanism of Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase, from its crystal structure in complex with reacted irreversible inhibitor 2-(2-phosphono-ethyl)-acrylic acid 4-nitro-phenyl ester

Released:
DOI: 10.2210/pdb1ml3/pdb
PDB entry 1ml3 coloured by chain, front view.
PDB entry 1ml3 coloured by chain, side view.
PDB entry 1ml3 coloured by chain, top view.
Source organism: Trypanosoma cruzi
Primary publication:
Evidence for the two phosphate binding sites of an analogue of the thioacyl intermediate for the Trypanosoma cruzi glyceraldehyde-3-phosphate dehydrogenase-catalyzed reaction, from its crystal structure.
Castilho MS, Pavão F, Oliva G, Ladame S, Willson M, Périé J
Biochemistry 42 7143-51 (2003)
PMID: 12795610

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 domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyceraldehyde-3-phosphate dehydrogenase, glycosomal Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 359 amino acids
Theoretical weight: 39.11 KDa
Source organism: Trypanosoma cruzi
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P22513 (Residues: 1-359; Coverage: 100%)
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 3 x NAD
1 bound ligand:
Ligand CYX 3 x CYX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: P21
Unit cell:
a: 81.456Å b: 85.259Å c: 105.153Å
α: 90° β: 95.61° γ: 90°
R-values:
R R work R free
0.199 0.199 0.264
Expression system: Escherichia coli BL21

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Citations

11 citation in other articles

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Depledge et al. (2010)
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5 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
4 more