› 6of5

X-ray diffraction
2.3Å resolution

The crystal structure of dodecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase

Released:
DOI: 10.2210/pdb6of5/pdb
PDB entry 6of5 coloured by chain, front view.
PDB entry 6of5 coloured by chain, side view.
PDB entry 6of5 coloured by chain, top view.
Source organism: Phaseolus vulgaris
Primary publication:
Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis.
Feder D, Kan MW, Hussein WM, Guddat LW, Schenk G, McGeary RP
Eur J Med Chem 182 111611 (2019)
PMID: 31445230

Function and Biology Details

Reaction catalysed: 
A phosphate monoester + H(2)O = an alcohol + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160393 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
Fe(3+)-Zn(2+) purple acid phosphatase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 426 amino acids
Theoretical weight: 49.56 KDa
Source organism: Phaseolus vulgaris
UniProt:
  • Canonical: P80366 (Residues: 34-459; Coverage: 98%)
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
9 bound ligands:
Ligand ZN 4 x ZN
Ligand FE 4 x FE
Ligand NAG 7 x NAG
Ligand SO4 19 x SO4
Ligand NA 5 x NA
Ligand EDO 14 x EDO
Ligand PGE 5 x PGE
Ligand MFJ 1 x MFJ
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P3121
Unit cell:
a: 126.808Å b: 126.808Å c: 298.211Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.179 0.231

Quick links

Citations

1 citations in other articles

Purple acid phosphatase 10c encodes a major acid phosphatase that regulates plant growth under phosphate-deficient conditions in rice.
Deng et al. (2020)