4DQM

Revealing a marine natural product as a novel agonist for retinoic acid receptors with a unique binding mode and antitumor activity

Structural Biology Knowledgebase: 4DQM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DQM

Classification: TRANSCRIPTION / TRANSFERASE

Total Structure Weight: 56092.04

Macromolecule Entities
Molecule Chains Length Organism Details
Retinoic acid receptor alpha A, C 234 Homo sapiens Fragment: ligand binding domain, UNP RESIDUES 182-415
Gene Name(s): RARA Gene View NR1B1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nuclear receptor coactivator 1 B, D 10 Homo sapiens EC#: 2.3.1.48 IUBMB
Fragment: LXXLL motif 7, UNP RESIDUES 1432-1441
Gene Name(s): NCOA1 Gene View BHLHE74 SRC1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C (5S)-4-[(3E,7E)-4,8-dimethyl-10-(2,6,6-trimethylcyclohex- 1-en-1-yl)deca-3,7-dien-1-yl]-5-hydroxyfuran- 2(5H)-one
Luffariellolide (Synonym)
C25 H38 O3
JPWPYTMXSXYUPG-XKILHPSWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.213
  • Space Group: P 2 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.12 α = 90.00
b = 104.46 β = 90.00
c = 113.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-16
  • Released Date: 2012-10-03
  • Deposition author(s): Wang, S., Wang, Z., Lin, S., Zheng, W., Wang, R., Jin, S., Chen, J., Jin, L., Li, Y.

Revision History

  • 2014-04-16
    Type: Experimental method | Details: update crystallization condition