2NSQ

Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein

• PDB DOI: https://doi.org/10.2210/pdb2NSQ/pdb

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


• Deposited: 2006-11-06 Released: 2006-12-19 
• 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: 1.85 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

The C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein

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: 18.09 kDa 
• Atom Count: 1,275 
• Modelled Residue Count: 140 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase NEDD4-like protein	A	155	Homo sapiens	Mutation(s): 0  Gene Names: NEDD4L, KIAA0439, NEDL3 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU5 (Homo sapiens) Explore Q96PU5  Go to UniProtKB:  Q96PU5
PHAROS:  Q96PU5 GTEx:  ENSG00000049759

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.93	α = 90
b = 60.036	β = 90
c = 74.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
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: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2013-08-28
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description