3DZU

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with BVT.13, 9-cis Retinoic Acid and NCOA2 Peptide

Structural Biology Knowledgebase: 3DZU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DZU

Classification: Transcription / DNA

Total Structure Weight: 116169.63


Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor RXR-alpha A 467 Homo sapiens Fragment: UNP residues 11-462
Gene Name(s): RXRA Gene View NR2B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Peroxisome proliferator-activated receptor gamma D 419 Homo sapiens Fragment: UNP residues 102-505
Gene Name(s): PPARG Gene View NR1C3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NCOA2 Peptide E, G 13 Homo sapiens Details: LxxLL motif peptide
Gene Name(s): NCOA2 Gene View BHLHE75 SRC2 TIF2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3') C 20 synthetic
DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3') F 20 synthetic

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

D 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN- 2-YLOXY)BENZOIC ACID
5-(2-PYRIMIDINYLOXY)-2-BENZOYLAMINOBENZOIC ACID (Synonym)
C18 H11 Cl2 N3 O4
VNDRRWBKNSHALL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
REA
Query on REA

A RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PLB EC50: 1300 nM (100) BindingDB
Ki: 100 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
REA IC50: >50000 nM (97) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.201
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 64.19 α = 70.95
b = 66.91 β = 82.56
c = 78.46 γ = 62.88

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-30
  • Released Date: 2008-10-28
  • Deposition author(s): Chandra, V., Huang, P., Hamuro, Y., Raghuram, S., Wang, Y., Burris, T.P., Rastinejad, F.

Revision History

  • 2012-05-16
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4