3WXF

Crystal structure of CYLD USP domain (C596S E674Q) in complex with Met1-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity

Sato, Y.Yamagata, A.Goto-Ito, S.Kubota, K.Fukai, S.

(2015) Nat.Struct.Mol.Biol. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, C
312Danio rerioMutation(s): 2 
Gene Names: cylda
Find proteins for E7FEV5 (Danio rerio)
Go to UniProtKB:  E7FEV5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
148Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.628α = 77.66
b = 65.372β = 89.04
c = 69.846γ = 89.46
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-30 
  • Released Date: 2015-02-11 
  • Deposition Author(s): Sato, Y., Fukai, S.

Revision History 

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Refinement description, Source and taxonomy