9C61

Crystal structure of the human LRRK2 WDR domain in complex with CACHE1193-26

• PDB DOI: https://doi.org/10.2210/pdb9C61/pdb

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


• Deposited: 2024-06-07 Released: 2024-07-03 
• Deposition Author(s): Zeng, H., Dong, A., Kutera, M., Ilyassov, O., Seitova, A., Loppnau, P., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Crystal structure of the human LRRK2 WDR domain in complex with CACHE1193-26

Zeng, H., Dong, A., Kutera, M., Ilyassov, O., Seitova, A., Loppnau, P., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

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)

Macromolecule Content

• Total Structure Weight: 87.97 kDa 
• Atom Count: 4,871 
• Modelled Residue Count: 639 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-specific serine/threonine protein kinase	A, B	389	Homo sapiens	Mutation(s): 0  Gene Names: LRRK2 EC: 2.7.11.1
UniProt
Find proteins for Q17RV3 (Homo sapiens) Explore Q17RV3  Go to UniProtKB:  Q17RV3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AUU (Subject of Investigation/LOI)	C [auth A], F [auth B]	(4R)-4-[4-(5-fluoro-1H-indol-3-yl)piperidine-1-carbonyl]piperidin-2-one C19 H22 F N3 O2 QDBIALQKWZMDJW-CYBMUJFWSA-N
UNX	D [auth A], E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.162	α = 90
b = 103.064	β = 90
c = 115.301	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Zeng, H., Dong, A., Kutera, M., Ilyassov, O., Seitova, A., Loppnau, P., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release