3IXP

Crystal structure of the ecdysone receptor bound to BYI08346

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.271 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EPHClick on this verticalbar to view detailsBest fitted 834Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history. 


Literature

Adaptability of the ecdysone receptor bound to synthetic ligands

Moras, D., Billas, I.M.L., Browning, C.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gene regulation protein263Heliothis virescensMutation(s): 0 
Gene Names: ecr
UniProt
Find proteins for Q7SIF6 (Heliothis virescens)
Explore Q7SIF6 
Go to UniProtKB:  Q7SIF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIF6
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ecdysone receptorB [auth D]265Helicoverpa armigeraMutation(s): 4 
Gene Names: usp
UniProt
Find proteins for B9UCQ4 (Helicoverpa armigera)
Explore B9UCQ4 
Go to UniProtKB:  B9UCQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9UCQ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPH
Query on EPH
Download Ideal Coordinates CCD File 
C [auth A]L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
C39 H68 N O8 P
MABRTXOVHMDVAT-AAEGOEIASA-N
834
Query on 834
Download Ideal Coordinates CCD File 
D
N-[2-(2-chlorophenyl)-4-methyl-5-(1-methylethyl)-1H-imidazol-1-yl]-5-methyl-2,3-dihydro-1,4-benzodioxine-6-carboxamide
C23 H24 Cl N3 O3
XLNQTHXOKGRTAL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.271 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.875α = 90
b = 147.875β = 90
c = 59.776γ = 120
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EPHClick on this verticalbar to view detailsBest fitted 834Click on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description