9GKG | pdb_00009gkg

Crystal structure of UNC119 in complex with Squarunkin A

• PDB DOI: https://doi.org/10.2210/pdb9GKG/pdb

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


• Deposited: 2024-08-24 Released: 2025-01-15 
• Deposition Author(s): Yelland, T., Ismail, S.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.227 (DCC) 

Starting Model: experimental

Literature

Crystal structure of UNC119 in complex with Squarunkin A

Yelland, T., Ismail, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 129.58 kDa 
• Atom Count: 8,663 
• Modeled Residue Count: 983 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein unc-119 homolog A	A [auth D], B [auth A], C [auth B], D [auth C], E, F [auth K]	182	Homo sapiens	Mutation(s): 0  Gene Names: UNC119, RG4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13432 (Homo sapiens) Explore Q13432  Go to UniProtKB:  Q13432
PHAROS:  Q13432 GTEx:  ENSG00000109103

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LRX (Subject of Investigation/LOI)	G [auth A], J [auth K]	squarunkin A C25 H32 F3 N5 O4 ZKITWOVRRSBKFG-UHFFFAOYSA-N
EDO	H [auth C], I [auth K]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.227 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.73	α = 90
b = 80.63	β = 90
c = 191.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Yelland, T., Ismail, S.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release