4NQA

Crystal structure of liganded hRXR-alpha/hLXR-beta heterodimer on DNA

Structural Biology Knowledgebase: 4NQA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 4NQA

Classification: TRANSCRIPTION REGULATOR / DNA

Total Structure Weight: 201037.22


Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor RXR-alpha A, H 365 Homo sapiens Fragment: UNP residues 98-462
Gene Name(s): RXRA Gene View NR2B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Liver X nuclear receptor beta B, I 391 Homo sapiens Fragment: UNP residues 72-461
Gene Name(s): NR1H2 Gene View LXRB NER UNR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nuclear receptor coactivator 2 C, D, J, K 13 Homo sapiens Fragment: peptide (UNP residues 686-698)
Gene Name(s): NCOA2 Gene View BHLHE75 SRC2 TIF2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*TP*AP*AP*GP*GP*TP*CP*AP*CP*TP*TP*CP*AP*GP*GP*TP*CP*A)-3' E, L 18 Synthetic construct DR4 DNA response element
5'-D(*TP*AP*TP*GP*AP*CP*CP*TP*GP*AP*AP*GP*TP*GP*AP*CP*CP*T)-3' F, M 18 Synthetic construct DR4 DNA response element

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
965
Query on 965

B, I [3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2- diphenylethyl)amino}propoxy)phenyl]acetic acid
C33 H31 Cl F3 N O3
NAXSRXHZFIBFMI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
9CR
Query on 9CR

A, H (9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, H, I ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
965 EC50: 20 - 501 nM (99 - 100) BindingDB
IC50: 7.9 - 40 nM (99 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.180
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 85.78 α = 90.00
b = 85.78 β = 90.00
c = 238.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-24
  • Released Date: 2014-02-26
  • Deposition author(s): Lou, X.H., Toresson, G., Benod, C., Suh, J.H., Phillips, K.J., Webb, P., Gustafsson, J.A.

Revision History

  • 2016-11-09
    Type: Source and taxonomy | Details: Corrected source information
  • 2016-11-09
    Type: Non-polymer description | Details: Corrected ligand REA to 9CR
  • 2014-03-19
    Type: Citation | Details: Citation update