3WJ5

Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin

PDB DOI: https://doi.org/10.2210/pdb3WJ5/pdb

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

Deposited: 2013-10-04 Released: 2014-10-15
Deposition Author(s): Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.247
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds

Harada, S., Hiromori, Y., Fukakusa, S., Kawahara, K., Nakamura, S., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Ohkubo, T., Yoshida, T., Nakanishi, T.

To be published.

Macromolecule Content

Total Structure Weight: 63.52 kDa
Atom Count: 4,419
Modelled Residue Count: 516
Deposited Residue Count: 552
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 gamma	A, B	276	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T9T Query on T9T 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]	triphenylstannanyl C₁₈ H₁₅ Sn NFHRNKANAAGQOH-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: 1.89 Å
R-Value Free: 0.247
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.521	α = 90
b = 88.492	β = 91.06
c = 57.943	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 2.0: 2019-06-12
Changes: Atomic model, Data collection
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Help and Resources

3WJ5

Crystal structure of PPARgamma ligand binding domain in complex with triphenyltin

Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds

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)