› 7xvz

X-ray diffraction
2.08Å resolution

Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile

Released:
DOI: 10.2210/pdb7xvz/pdb
PDB entry 7xvz coloured by chain, front view.
PDB entry 7xvz coloured by chain, side view.
PDB entry 7xvz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
Handa C, Yamazaki Y, Yonekubo S, Furuya N, Momose T, Ozawa T, Furuishi T, Fukuzawa K, Yonemochi E
J Steroid Biochem Mol Biol 222 106152 (2022)
PMID: 35810932

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172402 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Estrogen receptor beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 247 amino acids
Theoretical weight: 27.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92731 (Residues: 261-500; Coverage: 45%)
Gene names: ESR2, ESTRB, NR3A2
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Nuclear receptor coactivator 1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 13 amino acids
Theoretical weight: 1.39 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15788 (Residues: 630-640; Coverage: 1%)
Gene names: BHLHE74, NCOA1, SRC1

Ligands and Environments

1 bound ligand:
Ligand I1D 2 x I1D
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 51.728Å b: 88.58Å c: 101.252Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.267 0.241 0.307
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques.
Martin et al. (2024)
1 other article