3KMZ

Crystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 3KMZ

Classification: TRANSCRIPTION

Total Structure Weight: 66066.24

Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor alpha A, B 266 Homo sapiens Fragment: ligand binding domain
Gene Name(s): RARA Gene View NR1B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nuclear receptor corepressor 1 C, D 19 Homo sapiens Fragment: NR1
Gene Name(s): NCOR1 Gene View KIAA1047
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EQO
Query on EQO

A, B 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)- 5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid
C29 H24 O2
YCADIXLLWMXYKW-CMDGGOBGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EQO IC50: 114 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSO
Query on CSO
C, D L-PEPTIDE LINKING C3 H7 N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.172
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 104.83 α = 90.00
b = 105.63 β = 89.92
c = 53.38 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-11-11
  • Released Date: 2010-06-02
  • Deposition author(s): Bourguet, W., le Maire, A.

Revision History

  • 2011-07-13
    Type: Version format compliance