3LBD | pdb_00003lbd

LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO 9-CIS RETINOIC ACID

• PDB DOI: https://doi.org/10.2210/pdb3LBD/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: 2.40 Å
• R-Value Free: 
  0.267 (Depositor) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.172 (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: 30.49 kDa 
• Atom Count: 2,042 
• 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
9CR	B [auth A]	(9cis)-retinoic acid C20 H28 O2 SHGAZHPCJJPHSC-ZVCIMWCZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9CR	BindingDB:  3LBD	Ki: min: 0.5, max: 20 (nM) from 5 assay(s)
		Kd: min: 0.2, max: 150 (nM) from 9 assay(s)
		IC50: min: 7, max: 17 (nM) from 2 assay(s)
		EC50: min: 0.8, max: 74 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.267 (Depositor) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.666	α = 90
b = 60.666	β = 90
c = 155.134	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: 2016-11-16
  Changes: Non-polymer description
• Version 1.4: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection