5U3X
Human PPARdelta ligand-binding domain in complexed with specific agonist 8
- PDB DOI: https://doi.org/10.2210/pdb5U3X/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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.275
- R-Value Work: 0.217
- R-Value Observed: 0.219
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peroxisome proliferator-activated receptor delta | 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 AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 7U4 Query on 7U4 | C [auth A], I [auth B] | 6-[2-({cyclopropyl[4-(pyridin-3-yl)benzene-1-carbonyl]amino}methyl)phenoxy]hexanoic acid C28 H30 N2 O4 LNCQVUMJUZJEIR-UHFFFAOYSA-N |  | ||
| B7G Query on B7G | D [auth A], H [auth B] | heptyl beta-D-glucopyranoside C13 H26 O6 NIDYWHLDTIVRJT-UJPOAAIJSA-N |  | ||
| PEG Query on PEG | F [auth A], J [auth B], L [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| PGO Query on PGO | E [auth A], G [auth A], K [auth B], M [auth B], N [auth B] | S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.275
- R-Value Work: 0.217
- R-Value Observed: 0.219
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 39.1 | α = 90 |
| b = 92.94 | β = 98.03 |
| c = 96.16 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 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.
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
