3KMR

Crystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 3KMR

Classification: TRANSCRIPTION

Total Structure Weight: 31910.91

Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor alpha A 266 Homo sapiens Fragment: ligand binding domain (UNP RESIDUE 176-421)
Gene Name(s): RARA Gene View NR1B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nuclear receptor coactivator 1 C 13 Homo sapiens EC#: 2.3.1.48 IUBMB
Fragment: NR interaction motif 2 (UNP RESIDUE 686-698)
Gene Name(s): NCOA1 Gene View BHLHE74 SRC1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EQN
Query on EQN

A 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen- 2-yl)carbonyl]amino}benzoic acid
C22 H25 N O3
SZWKGOZKRMMLAJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EQN EC50: 0.3 - 79.43 nM (87 - 100) BindingDB
IC50: 41 nM (100) BindingDB
Kd: 36 - 1400 nM (87 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.197
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 88.31 α = 90.00
b = 61.22 β = 105.38
c = 49.44 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., Teyssier, C.

Revision History

  • Version 1_0: 2010-06-02

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance