3D5F | pdb_00003d5f

Crystal Structure of PPAR-delta complex

PDB DOI: https://doi.org/10.2210/pdb3D5F/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-05-16 Released: 2008-06-03
Deposition Author(s): Amano, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.281 (Depositor), 0.291 (DCC)
R-Value Work:
0.278 (Depositor), 0.285 (DCC)
R-Value Observed:
0.278 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3D5F

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

PPAR-Delta Activation Contributes to Neuroprotectio Against Thapsigargin-Induced SH-SY5Y Cell Death

Iwashita, A., Mihara, K., Amano, Y., Orita, M., Matsuoka, N.

To be published.

Macromolecule Content

Total Structure Weight: 61.94 kDa
Atom Count: 4,245
Modeled Residue Count: 508
Deposited Residue Count: 534
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	267	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181 Go to UniProtKB: Q03181
PHAROS: Q03181 GTEx: ENSG00000112033
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L41 Query on L41 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	{4-[3-(4-acetyl-3-hydroxy-2-propylphenoxy)propoxy]phenoxy}acetic acid C₂₂ H₂₆ O₇ HBBVCKCCQCQCTJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
L41	BindingDB: 3D5F	Kd: 76 (nM) from 1 assay(s)
		IC50: 13 (nM) from 1 assay(s)
		EC50: min: 6, max: 3800 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.281 (Depositor), 0.291 (DCC)
R-Value Work: 0.278 (Depositor), 0.285 (DCC)
R-Value Observed: 0.278 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.456	α = 90
b = 92.829	β = 98.02
c = 96.454	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.