4A4V

Ligand binding domain of human PPAR gamma in complex with amorfrutin 2

Structural Biology Knowledgebase: 4A4V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A4V

Classification: RECEPTOR

Total Structure Weight: 66001.01

Macromolecule Entities
Molecule Chains Length Organism Details
PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA A, B 287 Homo sapiens Fragment: LIGAND BINDING DOMAIN, RESIDUES 195-477
Gene Name(s): PPARG Gene View NR1C3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B AMORFRUTIN 2
C18 H26 O4
UJSSSFNGQWZNEN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
YFD EC50: 1200 nM (99) BindingDB
Kd: 287 nM (99) BindingDB

N/A in BindingMoad
Kd: 287 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.209
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.29 α = 90.00
b = 60.97 β = 102.65
c = 117.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-20
  • Released Date: 2012-10-03
  • Deposition author(s): de Groot, J.C., Weidner, C., Krausze, J., Kawamoto, K., Schroeder, F.C., Sauer, S., Buessow, K.

Revision History

  • 2014-02-05
    Type: Citation | Details: JRNL