Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 211864.89 
• Atom Count: 14395 
• Residue Count: 1848 
• Unique protein chains: 2

5ZQ6

SidE-Ubi-ADPr

• DOI: 10.2210/pdb5ZQ6/pdb

• Classification: CELL INVASION
• Organism(s): Homo sapiens, Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2018-04-17 Released: 2018-05-23 
• Deposition Author(s): Wang, Y., Gao, A., Gao, P.
• Funding Organization(s): null 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.009 Å
• R-Value Free: 0.232 
• R-Value Work: 0.180 

Literature

Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.

Wang, Y., Shi, M., Feng, H., Zhu, Y., Liu, S., Gao, A., Gao, P.

(2018) Cell 173: 1231-1243.e16

• PubMed: 29731171 
• Primary Citation of Related Structures:  
  5ZQ7, 5ZQ5, 5ZQ4, 5ZQ3, 5ZQ2

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SidE	A, C	845	Legionella pneumophila	Mutation(s): 0  Gene Names: laiD
Find proteins for Q6BBR6 (Legionella pneumophila) Go to UniProtKB:  Q6BBR6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	B, D	79	Homo sapiens	Mutation(s): 1  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
ADP	A, C	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.009 Å
• R-Value Free: 0.232 
• R-Value Work: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 92.322	α = 90.00
b = 128.003	β = 90.00
c = 191.065	γ = 90.00

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
PHENIX	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-04-17 
• Released Date: 2018-05-23 
• Deposition Author(s): Wang, Y., Gao, A., Gao, P.

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Funding Organization	Location	Grant Number
	China	91753133
	China	31670903
	China	31700687
	China	XDB08020204

Revision History 

• Version 1.0: 2018-05-23
  Type: Initial release
• Version 1.1: 2018-05-30
  Type: Data collection, Database references