› 1rdt

X-ray diffraction
2.4Å resolution

Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the RXRalpha/PPARgamma heterodimer

Released:
DOI: 10.2210/pdb1rdt/pdb
PDB entry 1rdt coloured by chain, front view.
PDB entry 1rdt coloured by chain, side view.
PDB entry 1rdt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of potent retinoid X receptor alpha agonists.
Haffner CD, Lenhard JM, Miller AB, McDougald DL, Dwornik K, Ittoop OR, Gampe RT, Xu HE, Blanchard S, Montana VG, Consler TG, Bledsoe RK, Ayscue A, Croom D
J Med Chem 47 2010-29 (2004)
PMID: 15056000

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148712 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Retinoic acid receptor RXR-alpha Chain: A
Molecule details ›
Chain: A
Length: 242 amino acids
Theoretical weight: 27.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19793 (Residues: 225-462; Coverage: 52%)
Gene names: NR2B1, RXRA
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
Nuclear receptor coactivator 1 Chain: B
Molecule details ›
Chain: B
Length: 25 amino acids
Theoretical weight: 2.81 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15788 (Residues: 676-700; Coverage: 2%)
Gene names: BHLHE74, NCOA1, SRC1
Sequence domains: Steroid receptor coactivator
Peroxisome proliferator-activated receptor gamma Chain: D
Molecule details ›
Chain: D
Length: 284 amino acids
Theoretical weight: 32.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37231 (Residues: 235-505; Coverage: 54%)
Gene names: NR1C3, PPARG
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
CREB-binding protein Chain: E
Molecule details ›
Chain: E
Length: 23 amino acids
Theoretical weight: 2.37 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q92793 (Residues: 58-80; Coverage: 1%)
Gene names: CBP, CREBBP

Ligands and Environments

2 bound ligands:
Ligand L79 1 x L79
Ligand 570 1 x 570
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 49.69Å b: 54.58Å c: 211.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.221 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Triterpenoids and rexinoids as multifunctional agents for the prevention and treatment of cancer.
Liby et al. (2007)
5 more

16 mentions without citation

The retinoid X receptors and their ligands.
Dawson et al. (2012)
15 more