› 1xx1

X-ray diffraction
1.75Å resolution

Structural basis for ion-coordination and the catalytic mechanism of sphingomyelinases D

Released:
DOI: 10.2210/pdb1xx1/pdb
PDB entry 1xx1 coloured by chain, front view.
PDB entry 1xx1 coloured by chain, side view.
PDB entry 1xx1 coloured by chain, top view.
Source organism: Loxosceles laeta
Primary publication:
Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D.
Murakami MT, Fernandes-Pedrosa MF, Tambourgi DV, Arni RK
J Biol Chem 280 13658-64 (2005)
PMID: 15654080

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-184723 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dermonecrotic toxin LlSicTox-alphaIII1i Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 285 amino acids
Theoretical weight: 32.08 KDa
Source organism: Loxosceles laeta
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8I914 (Residues: 27-311; Coverage: 98%)
Structure domains: Phosphatidylinositol (PI) phosphodiesterase

Ligands and Environments

3 bound ligands:
Ligand SO4 23 x SO4
Ligand MG 4 x MG
Ligand EPE 3 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE D03B-MX1
Spacegroup: P65
Unit cell:
a: 139.818Å b: 139.818Å c: 113.461Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.186 0.225
Expression system: Escherichia coli BL21

Quick links

Citations

6 review citations

Phospholipase D: enzymology, functionality, and chemical modulation.
Selvy et al. (2011)
5 more

15 mentions without citation

Bacterial Sphingomyelinases and Phospholipases as Virulence Factors.
Flores-Díaz et al. (2016)
14 more