8UXS

KLHDC2 ubiquitin ligase in complex with a novel small-molecule

• PDB DOI: https://doi.org/10.2210/pdb8UXS/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-11-10 Released: 2024-07-10 
• Deposition Author(s): Rusnac, D.V., Zheng, N.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

KLHDC2 ubiquitin ligase in complex with a novel small-molecule

Rusnac, D.V., Zhou, G., Canzani, D., Bush, M.F., DiMaio, F., Zheng, N.

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.

Macromolecule Content

• Total Structure Weight: 78.75 kDa 
• Atom Count: 5,497 
• Modelled Residue Count: 644 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein 2	A, B	341	Homo sapiens	Mutation(s): 0  Gene Names: KLHDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U9 (Homo sapiens) Explore Q9Y2U9  Go to UniProtKB:  Q9Y2U9
GTEx:  ENSG00000165516

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XU8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	{4-[(2-{[(4-tert-butylphenyl)methyl]sulfanyl}acetamido)methyl]-1H-1,2,3-triazol-1-yl}acetic acid C18 H24 N4 O3 S HCTZVVOCYIXIAH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.381	α = 90
b = 88.165	β = 104.39
c = 88.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Rusnac, D.V., Zheng, N.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release