Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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: 20318.94 
• Atom Count: 1391 
• Residue Count: 191 
• Unique protein chains: 1

6M8Z

Crystal structure of human DJ-1 without a modification on Cys-106

• DOI: 10.2210/pdb6M8Z/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2018-08-22 Released: 2018-09-05 
• Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Shumilina, S.V., Werenskjold, C., Utepbergenov, D., Minor, W.
• Funding Organization(s): null; National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 

Literature

A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1.

Mussakhmetov, A., Shumilin, I.A., Nugmanova, R., Shabalin, I.G., Baizhumanov, T., Toibazar, D., Khassenov, B., Minor, W., Utepbergenov, D.

(2018) Biochem. Biophys. Res. Commun. 504: 328-333

• PubMed: 30190129 
• Primary Citation of Related Structures:  
  6E5Z

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein/nucleic acid deglycase DJ-1	A	191	Homo sapiens	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• Space Group: P 6₅ 2 2
• Diffraction Data DOI: 
  10.18430/m36m8z Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 66.500	α = 90.00
b = 66.500	β = 90.00
c = 176.728	γ = 120.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-22 
• Released Date: 2018-09-05 
• Deposition Author(s): Shumilin, I.A., Shabalin, I.G., Shumilina, S.V., Werenskjold, C., Utepbergenov, D., Minor, W.

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Funding Organization	Location	Grant Number
	Kazakhstan	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	--

Revision History 

• Version 1.0: 2018-09-05
  Type: Initial release
• Version 1.1: 2018-09-19
  Type: Data collection, Database references