9M2E | pdb_00009m2e

Crystal Structure of Nur77 LBD in complex with DBIC compound

• PDB DOI: https://doi.org/10.2210/pdb9M2E/pdb

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


• Deposited: 2025-02-27 Released: 2025-12-03 
• Deposition Author(s): Hong, W.B., Lin, T.W., Chen, X.Q., Wu, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.209 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of Nur77 LBD in complex with DBIC compound

Wu, L.Z., Hong, W.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.42 kDa 
• Atom Count: 3,701 
• Modeled Residue Count: 456 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 4immunitygroup A member 1	A [auth BBB], B [auth AAA]	248	Homo sapiens	Mutation(s): 0  Gene Names: NR4A1, GFRP1, HMR, NAK1
UniProt & NIH Common Fund Data Resources
Find proteins for P22736 (Homo sapiens) Explore P22736  Go to UniProtKB:  P22736
PHAROS:  P22736 GTEx:  ENSG00000123358

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D7W (Subject of Investigation/LOI)	C [auth AAA]	dodecyl 1H-benzimidazole-5-carboxylate C20 H30 N2 O2 VXKKXAFRWVJMCS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.209 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.522	α = 90
b = 76.094	β = 90
c = 128.273	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Hong, W.B., Lin, T.W., Chen, X.Q., Wu, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release