2NQ3

Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase

• PDB DOI: https://doi.org/10.2210/pdb2NQ3/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2006-10-30 Released: 2006-11-14 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

The C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase

Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.24 kDa 
• Atom Count: 1,192 
• Modelled Residue Count: 131 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Itchy homolog E3 ubiquitin protein ligase	A	173	Homo sapiens	Mutation(s): 0  Gene Names: ITCH EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96J02 (Homo sapiens) Explore Q96J02  Go to UniProtKB:  Q96J02
PHAROS:  Q96J02 GTEx:  ENSG00000078747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.195 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.499	α = 90
b = 82.499	β = 90
c = 65.273	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description