Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52532.38 
• Atom Count: 3080 
• Residue Count: 465 
• Unique protein chains: 2

6GLC

Structure of phospho-Parkin bound to phospho-ubiquitin

• DOI: 10.2210/pdb6GLC/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2018-05-23 Released: 2018-06-13 
• Deposition Author(s): Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.
• Funding Organization(s): Medical Research Council (United Kingdom); European Research Council; Michael J. Fox Foundation 

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 

Literature

Mechanism of parkin activation by PINK1.

Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.

(2018) Nature 559: 410-414

• PubMed: 29995846 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase parkin	A	389	Homo sapiens	Mutation(s): 1  Gene Names: PRKN (PARK2) EC: 2.3.2.31
Find proteins for O60260 (Homo sapiens) Go to Gene View: PRKN Go to UniProtKB:  O60260

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
3CN	B	NON-POLYMER	C3 H9 N		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 83.931	α = 90.00
b = 83.931	β = 90.00
c = 105.119	γ = 120.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-23 
• Released Date: 2018-06-13 
• Deposition Author(s): Gladkova, C., Maslen, S.L., Skehel, J.M., Komander, D.

---

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105192732
European Research Council	United Kingdom	309756
European Research Council	United Kingdom	724804
Michael J. Fox Foundation	United Kingdom	--

Revision History 

• Version 1.0: 2018-06-13
  Type: Initial release
• Version 1.1: 2018-07-18
  Type: Data collection, Database references
• Version 1.2: 2018-08-01
  Type: Data collection, Database references