8PIF | pdb_00008pif

Fragment 12 in complex with KLHDC2

• PDB DOI: https://doi.org/10.2210/pdb8PIF/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-06-21 Released: 2023-07-12 
• Deposition Author(s): Boettcher, J., Mayer, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

KLHDC2 - The Next Level

Boettcher, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.02 kDa 
• Atom Count: 5,662 
• Modeled Residue Count: 632 
• Deposited Residue Count: 726 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch domain-containing protein 2	A, B	363	Homo sapiens	Mutation(s): 0  Gene Names: KLHDC2, HCA33
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U9 (Homo sapiens) Explore Q9Y2U9  Go to UniProtKB:  Q9Y2U9
PHAROS:  Q9Y2U9 GTEx:  ENSG00000165516

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YW6 (Subject of Investigation/LOI)	D [auth A], E [auth B]	2-(furan-3-yl)ethanoic acid C6 H6 O3 UUUYAVXPERPSAI-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.261	α = 90
b = 88.308	β = 104.51
c = 88.922	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Boettcher, J., Mayer, M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection