2ONI

Catalytic Domain of the Human NEDD4-like E3 Ligase

Structural Biology Knowledgebase: 2ONI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ONI

Classification: LIGASE

Total Structure Weight: 47271.09

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase NEDD4-like protein A 392 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: Hect Domain (ubiquitin transferase)
Mutation: M600M, M616M, M655M, M718M, M719M, M729M, M754M, M778M, M804M, M832M, M870M, M890M, M943M
Gene Name(s): NEDD4L Gene View KIAA0439 NEDL3

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.206
  • Space Group: P 63 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.06 α = 90.00
b = 103.06 β = 90.00
c = 182.21 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-24
  • Released Date: 2007-04-17
  • Deposition author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4