3IXP | pdb_00003ixp

Crystal structure of the ecdysone receptor bound to BYI08346

PDB DOI: https://doi.org/10.2210/pdb3IXP/pdb

Classification: TRANSCRIPTION
Organism(s): Heliothis virescens, Helicoverpa armigera
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-09-04 Released: 2010-12-15
Deposition Author(s): Moras, D., Billas, I.M.L., Browning, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.271 (Depositor), 0.257 (DCC)
R-Value Work:
0.221 (Depositor), 0.209 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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.

Macromolecule Content

Total Structure Weight: 61.29 kDa
Atom Count: 3,811
Modeled Residue Count: 462
Deposited Residue Count: 528
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gene regulation protein	A	263	Heliothis virescens	Mutation(s): 0 Gene Names: ecr
UniProt
Find proteins for Q7SIF6 (Heliothis virescens) Explore Q7SIF6 Go to UniProtKB: Q7SIF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIF6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ecdysone receptor	B [auth D]	265	Helicoverpa armigera	Mutation(s): 4 Gene Names: usp
UniProt
Find proteins for B9UCQ4 (Helicoverpa armigera) Explore B9UCQ4 Go to UniProtKB: B9UCQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9UCQ4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPH Query on EPH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE C₃₉ H₆₈ N O₈ P MABRTXOVHMDVAT-AAEGOEIASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
834 Query on 834 Download:Ideal Coordinates CCD File SDF format, chain D MOL2 format, chain D mmCIF format, chain D	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		Interactions Focus chain D Interactions & Density Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.271 (Depositor), 0.257 (DCC)
R-Value Work: 0.221 (Depositor), 0.209 (DCC)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.875	α = 90
b = 147.875	β = 90
c = 59.776	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.