7AHJ | pdb_00007ahj

Crystal structure of PPARgamma V290M mutant ligand binding domain in complex with farglitazar

PDB DOI: https://doi.org/10.2210/pdb7AHJ/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-09-24 Released: 2020-10-14
Deposition Author(s): Schoenmakers, E., Schwabe, B.T.W., Fairall, L., Chatterjee, K., Schwabe, J.W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.200 (Depositor), 0.202 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of PPARgamma V290M mutant ligand binding domain in complex with farglitazar

Schoenmakers, E., Schwabe, B.T.W., Fairall, L., Chatterjee, K., Schwabe, J.W.R.

To be published.

Macromolecule Content

Total Structure Weight: 63.4 kDa
Atom Count: 4,309
Modeled Residue Count: 524
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	275	Homo sapiens	Mutation(s): 1 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
570 Query on 570 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-(2-BENZOYL-PHENYLAMINO)-3-{4-[2-(5-METHYL-2-PHENYL-OXAZOL-4-YL)-ETHOXY]-PHENYL}-PROPIONIC ACID C₃₄ H₃₀ N₂ O₅ ZZCHHVUQYRMYLW-HKBQPEDESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.200 (Depositor), 0.202 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.96	α = 90
b = 61.24	β = 103.17
c = 118.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
SCALA	data scaling
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

Schoenmakers, E.

Schwabe, B.T.W.

Schwabe, J.W.R.

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, 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.