5U3Y

Human PPARdelta ligand-binding domain in complexed with specific agonist 9

PDB DOI: https://doi.org/10.2210/pdb5U3Y/pdb

Classification: protein binding/activator
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-12-03 Released: 2017-03-22
Deposition Author(s): Wu, C.-C., Baiga, T.J., Downes, M., La Clair, J.J., Atkins, A.R., Richard, S.B., Stockley-Noel, T.A., Bowman, M.E., Evans, R.M., Noel, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.246
R-Value Work: 0.203
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 64.55 kDa
Atom Count: 4,505
Modelled Residue Count: 518
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	272	Homo sapiens	Mutation(s): 0 Gene Names: PPARD, NR1C2, PPARB
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7U7 Query on 7U7 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B]	D [auth A], J [auth B]	6-[2-({cyclopropyl[4-(furan-2-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid C₂₇ H₂₉ N O₅ CQKNIDGIDMCYLZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
B7G Query on B7G Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth A]	C [auth A], I [auth A]	heptyl beta-D-glucopyranoside C₁₃ H₂₆ O₆ NIDYWHLDTIVRJT-UJPOAAIJSA-N		Interactions Focus chain C [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain I [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B]	G [auth A] H [auth A] L [auth B] M [auth B] N [auth B] G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
PGO Query on PGO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	E [auth A], F [auth A], K [auth B]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
7U7	BindingDB: 5U3Y	EC50: min: 4.81, max: 20 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.246
R-Value Work: 0.203
R-Value Observed: 0.204
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.44	α = 90
b = 94.94	β = 97.53
c = 96.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2017-03-29
Changes: Database references
Version 1.2: 2017-04-05
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

5U3Y

Human PPARdelta ligand-binding domain in complexed with specific agonist 9

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)