3B7Y

Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4

• PDB DOI: https://doi.org/10.2210/pdb3B7Y/pdb

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


• Deposited: 2007-10-31 Released: 2007-11-27 
• Deposition Author(s): Walker, J.R., Ruzanov, M., Butler-Cole, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

C2 Domain of the Human E3 Ubiquitin-Protein Ligase NEDD4.

Walker, J.R., Ruzanov, M., Butler-Cole, C., Weigelt, J., 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.58 kDa 
• Atom Count: 2,553 
• Modelled Residue Count: 290 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase NEDD4	A, B	153	Homo sapiens	Mutation(s): 0  Gene Names: NEDD4, KIAA0093 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P46934 (Homo sapiens) Explore P46934  Go to UniProtKB:  P46934
PHAROS:  P46934 GTEx:  ENSG00000069869

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.778	α = 108.89
b = 47.997	β = 111.11
c = 50.786	γ = 100.86

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: 2007-11-27 
Deposition Author(s): Walker, J.R., Ruzanov, M., Butler-Cole, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description