4LBD | pdb_00004lbd

LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO THE SYNTHETIC AGONIST BMS961

• PDB DOI: https://doi.org/10.2210/pdb4LBD/pdb

• Classification: NUCLEAR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-02-04 Released: 1999-03-02 
• Deposition Author(s): Klaholz, B.P., Renaud, J.-P., Mitschler, A., Moras, D., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.285 (Depositor) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Conformational adaptation of agonists to the human nuclear receptor RAR gamma.

Klaholz, B.P., Renaud, J.P., Mitschler, A., Zusi, C., Chambon, P., Gronemeyer, H., Moras, D.

(1998) Nat Struct Biol 5: 199-202

• PubMed: 9501913 
• DOI: https://doi.org/10.1038/nsb0398-199
• Primary Citation Related Structures: 
  3LBD, 4LBD

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Organizational Affiliation: 
• Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Illkirch, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.59 kDa 
• Atom Count: 2,002 
• Modeled Residue Count: 237 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RETINOIC ACID RECEPTOR GAMMA	A	267	Homo sapiens	Mutation(s): 0  Gene Names: HRARGAMMA
UniProt & NIH Common Fund Data Resources
Find proteins for P13631 (Homo sapiens) Explore P13631  Go to UniProtKB:  P13631
PHAROS:  P13631 GTEx:  ENSG00000172819

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
961	B [auth A]	3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID C23 H26 F N O4 AANFHDFOMFRLLR-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.285 (Depositor) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.882	α = 90
b = 59.882	β = 90
c = 155.958	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MARXDS	data reduction
MARSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-02 
Deposition Author(s): Klaholz, B.P., Renaud, J.-P., Mitschler, A., Moras, D., Structural Proteomics in Europe (SPINE)

Revision History  

• Version 1.0: 1999-03-02
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection