6OJE | pdb_00006oje

Dimeric structure of LRRK2 GTPase domain

• PDB DOI: https://doi.org/10.2210/pdb6OJE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-11 Released: 2020-10-14 
• Deposition Author(s): Hoang, Q.Q., Wu, C.X., Liao, J., Park, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical basis of ROC-dependent activation of LRRK2

Park, Y., Wu, C., Tennessen, K., Wan, L., Hoang, N.C., Hoang, C.W., Liao, J., Hoang, Q.Q.

(2026) PNAS Nexus 

• DOI: https://doi.org/10.1093/pnasnexus/pgag112

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: 48.01 kDa 
• Atom Count: 3,296 
• Modeled Residue Count: 373 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat serine/threonine-protein kinase 2	A, B	206	Homo sapiens	Mutation(s): 0  Gene Names: LRRK2, PARK8 EC: 2.7.11.1 (PDB Primary Data), 3.6.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5S007 (Homo sapiens) Explore Q5S007  Go to UniProtKB:  Q5S007
PHAROS:  Q5S007 GTEx:  ENSG00000188906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A], E [auth A], F [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.647	α = 90
b = 103.688	β = 101.2
c = 44.593	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Hoang, Q.Q., Wu, C.X., Liao, J., Park, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM111639
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115844

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2026-04-22
  Changes: Database references, Structure summary