› 2pt9

X-ray diffraction
2.2Å resolution

The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4-methylcyclohexylamine (4MCHA)

Released:
DOI: 10.2210/pdb2pt9/pdb
PDB entry 2pt9 coloured by chain, front view.
PDB entry 2pt9 coloured by chain, side view.
PDB entry 2pt9 coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.
Dufe VT, Qiu W, Müller IB, Hui R, Walter RD, Al-Karadaghi S
J Mol Biol 373 167-77 (2007)
PMID: 17822713

Function and Biology Details

Reaction catalysed: 
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184780 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PABS domain-containing protein Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 321 amino acids
Theoretical weight: 36.64 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8II73 (Residues: 1-321; Coverage: 100%)
Gene name: PF3D7_1129000
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand S4M 3 x S4M
Ligand 2MH 3 x 2MH
Ligand 1PG 2 x 1PG
Ligand GOL 3 x GOL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I911-2
Spacegroup: C2
Unit cell:
a: 196.24Å b: 134.1Å c: 48.35Å
α: 90° β: 94.53° γ: 90°
R-values:
R R work R free
0.2 0.196 0.239
Expression system: Escherichia coli

Quick links

Citations

8 review citations

Spermine synthase.
Pegg et al. (2010)
7 more

7 mentions without citation

Benefits of structural genomics for drug discovery research.
Grabowski et al. (2009)
6 more