5YD6 | pdb_00005yd6

Crystal structure of PG-bound Nurr1-LBD

• PDB DOI: https://doi.org/10.2210/pdb5YD6/pdb

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


• Deposited: 2017-09-11 Released: 2019-03-27 
• Deposition Author(s): Sreekanth, R., Yoon, H.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.225 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Structure of Nurr1 bound to cyclopentenone prostaglandin A2 and its mechanism of action in ameliorating dopaminergic neurodegeneration in Drosophila

Rajan, S., Toh, H.T., Lim, K.H., Yoon, H.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.69 kDa 
• Atom Count: 7,624 
• Modeled Residue Count: 901 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4 group A member 2	A, B, C, D	271	Homo sapiens	Mutation(s): 0  Gene Names: NR4A2, NOT, NURR1, TINUR
UniProt & NIH Common Fund Data Resources
Find proteins for P43354 (Homo sapiens) Explore P43354  Go to UniProtKB:  P43354
PHAROS:  P43354 GTEx:  ENSG00000153234

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8SU (Subject of Investigation/LOI)	E [auth A], H [auth B], I [auth C], J [auth D]	(~{Z})-7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]hept-5-enoic acid C20 H30 O4 MYHXHCUNDDAEOZ-FOSBLDSVSA-N
MG	F [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.269 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.225 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.95	α = 90
b = 94.08	β = 90
c = 135.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Sreekanth, R., Yoon, H.S.

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary