1M13

Crystal Structure of the Human Pregane X Receptor Ligand Binding Domain in Complex with Hyperforin, a Constituent of St. John's Wort

Structural Biology Knowledgebase: 1M13 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.212

Literature

Macromolecules
Sequence Display for 1M13

Classification: TRANSCRIPTION

Total Structure Weight: 36817.95

Macromolecule Entities
Molecule Chains Length Organism Details
Orphan Nuclear Receptor PXR A 316 Homo sapiens Fragment: Includes Ligand Binding Domain (Residues 130-434)
Gene Name(s): NR1I2 Gene View PXR
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 4-HYDROXY-5-ISOBUTYRYL-6-METHYL-1,3,7-TRIS- (3-METHYL-BUT-2-ENYL)-6-(4-METHYL-PENT-3- ENYL)-BICYCLO[3.3.1]NON-3-ENE-2,9-DIONE
HYPERFORIN (Synonym)
C35 H52 O4
IWBJJCOKGLUQIZ-OJCNYLSASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HYF N/A in BindingDB
Kd: 27 nM  BindingMOAD
Kd: 27 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.212
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.37 α = 90.00
b = 91.37 β = 90.00
c = 85.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-17
  • Released Date: 2003-03-04
  • Deposition author(s): Watkins, R.E., Maglich, J.M., Moore, L.B., Wisely, G.B., Noble, S.M., Davis-Searles, P.R., Lambert, M.H., Kliewer, S.A., Redinbo, M.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4