Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2BC 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 71885.83 
• Atom Count: 4978 
• Residue Count: 630 
• Unique protein chains: 4

6N13

UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin

• DOI: 10.2210/pdb6N13/pdb
• BMRB: 27664

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2018-11-08 Released: 2018-11-28 
• Deposition Author(s): Condos, T.E.C., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.
• Funding Organization(s): Canadian Institutes of Health Research 

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.

Condos, T.E., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.

(2018) EMBO J. 37: --

• PubMed: 30446597 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
E3 ubiquitin-protein ligase parkin	B	322	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
ubiquitin	D	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 L3	C	156	Homo sapiens	Mutation(s): 3  Gene Names: UBE2L3 (UBCE7, UBCH7) EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens) Go to Gene View: UBE2L3 Go to UniProtKB:  P68036

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
phosphoubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-08 
• Released Date: 2018-11-28 
• Deposition Author(s): Condos, T.E.C., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research	Canada	MOP-14606

Revision History 

• Version 1.0: 2018-11-28
  Type: Initial release
• Version 1.1: 2018-12-12
  Type: Data collection, Database references