8Z5A | pdb_00008z5a

Crystal Structure of Nur77 LBD in complex with NLM1

• PDB DOI: https://doi.org/10.2210/pdb8Z5A/pdb

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


• Deposited: 2024-04-18 Released: 2025-04-23 
• Deposition Author(s): Hong, W.B., Lin, T.W., Chen, X.Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Nur77 LBD in complex with NLM1

Hong, W.B., Lin, T.W., Chen, X.Q.

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: 55.68 kDa 
• Atom Count: 3,693 
• Modeled Residue Count: 455 
• 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 B], B [auth A]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D72 (Subject of Investigation/LOI)	D [auth A]	5-[[4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidin-2-yl]amino]-~{N}-(3-morpholin-4-ylpropyl)-1~{H}-indole-2-carboxamide C25 H30 N8 O2 S OTGQZMLMXDRMMX-UHFFFAOYSA-N
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.274 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.463	α = 90
b = 76.435	β = 90
c = 127.866	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: 2025-04-23 
Deposition Author(s): Hong, W.B., Lin, T.W., Chen, X.Q.

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

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release