› 3up3

X-ray diffraction
1.25Å resolution

Nuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in complex with (25S)-cholestenoic acid

Released:
DOI: 10.2210/pdb3up3/pdb
PDB entry 3up3 coloured by chain, front view.
PDB entry 3up3 coloured by chain, side view.
PDB entry 3up3 coloured by chain, top view.
Source organisms:
Primary publication:
Structural conservation of ligand binding reveals a bile acid-like signaling pathway in nematodes.
Zhi X, Zhou XE, Melcher K, Motola DL, Gelmedin V, Hawdon J, Kliewer SA, Mangelsdorf DJ, Xu HE
J Biol Chem 287 4894-903 (2012)
PMID: 22170062

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124706 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NR LBD domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 243 amino acids
Theoretical weight: 27.77 KDa
Source organism: Ancylostoma ceylanicum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H0USY8 (Residues: 1-243; Coverage: 100%)
Gene name: daf-12
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
Nuclear receptor coactivator 2 Chain: P
Molecule details ›
Chain: P
Length: 14 amino acids
Theoretical weight: 1.68 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15596 (Residues: 741-754; Coverage: 1%)
Gene names: BHLHE75, NCOA2, SRC2, TIF2

Ligands and Environments

2 bound ligands:
Ligand XCA 1 x XCA
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 34.545Å b: 85.296Å c: 46.325Å
α: 90° β: 106.87° γ: 90°
R-values:
R R work R free
0.167 0.166 0.18
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Interspecific communication between pinewood nematode, its insect vector, and associated microbes.
Zhao et al. (2014)
4 more

4 mentions without citation

Benchmarking of different molecular docking methods for protein-peptide docking.
Agrawal et al. (2019)
3 more