3NOA | pdb_00003noa

Crystal structure of human PPAR-gamma ligand binding domain complex with a potency improved agonist

PDB DOI: https://doi.org/10.2210/pdb3NOA/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-25 Released: 2011-06-29
Deposition Author(s): Peng, Y.H., Wu, J.S., Wu, S.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.275 (Depositor), 0.273 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of human PPAR-gamma ligand binding domain complex with a potency improved agonist

Peng, Y.H., Coumar, M.S., Leou, J.S., Wu, J.S., Shiao, H.Y., Lin, C.H., Lyu, P.C., Hsieh, H.P., Wu, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 63.09 kDa
Atom Count: 4,520
Modeled Residue Count: 542
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	271	Homo sapiens	Mutation(s): 0 Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231 Go to UniProtKB: P37231
PHAROS: P37231 GTEx: ENSG00000132170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5BC Query on 5BC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(5-{3-[4-(biphenyl-4-ylcarbonyl)-2-propylphenoxy]propoxy}-1H-indol-1-yl)acetic acid C₃₅ H₃₃ N O₅ KDJDNXXKJABUHE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.275 (Depositor), 0.273 (DCC)
R-Value Work: 0.231 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.404	α = 90
b = 87.744	β = 90.73
c = 57.674	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.