4A4W

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

Structural Biology Knowledgebase: 4A4W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4A4W

Classification: RECEPTOR

Total Structure Weight: 66205.27

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

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

A, B AMORFRUTIN B
C26 H32 O4
DKNIJLWIVUCTHW-CPNJWEJPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
YFB N/A in BindingDB
N/A in BindingMoad
Kd: 19 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.203
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.14 α = 90.00
b = 60.86 β = 102.58
c = 117.60 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