Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
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: 20308.83 
• Atom Count: 1452 
• Residue Count: 189 
• Unique protein chains: 1

6AFB

DJ-1 C106S incubated with isatin

• DOI: 10.2210/pdb6AFB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): 1 


• Deposited: 2018-08-08 Released: 2018-08-29 
• Deposition Author(s): Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan); Japan Society for the Promotion of Science 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 

Literature

Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.

Tashiro, S., Caaveiro, J.M.M., Nakakido, M., Tanabe, A., Nagatoishi, S., Tamura, Y., Matsuda, N., Liu, D., Hoang, Q.Q., Tsumoto, K.

(2018) ACS Chem. Biol. 13: 2783-2793

• PubMed: 30063823 
• Primary Citation of Related Structures:  
  6AFL, 6AFJ, 6AFI, 6AFH, 6AFG, 6AFF, 6AFE, 6AFD, 6AFC, 6AFA, 6AF9, 6AF7, 6AF5

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein/nucleic acid deglycase DJ-1	A	189	Homo sapiens	Mutation(s): 1  Gene Names: PARK7 EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens) Go to Gene View: PARK7 Go to UniProtKB:  Q99497

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ISN	A	ISATIN C8 H5 N O2 JXDYKVIHCLTXOP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.860	α = 90.00
b = 74.860	β = 90.00
c = 74.690	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
SCALA	data scaling
MOSFLM	data reduction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-08 
• Released Date: 2018-08-29 
• Deposition Author(s): Caaveiro, J.M.M., Tashiro, S., Tsumoto, K.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	Platform for Drug Discovery, Informatics and Structural Life Science
Japan Society for the Promotion of Science	Japan	25249115
Japan Society for the Promotion of Science	Japan	16H02420
Japan Society for the Promotion of Science	Japan	15K06962

Revision History 

• Version 1.0: 2018-08-29
  Type: Initial release
• Version 1.1: 2018-10-03
  Type: Data collection, Database references