5XIT

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.

Takahashi, T.S.Hirade, Y.Toma, A.Sato, Y.Yamagata, A.Goto-Ito, S.Tomita, A.Nakada, S.Fukai, S.

(2018) Nat Commun 9: 170-170


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
D, F
76Mus musculusMutation(s): 1 
Gene Names: Rps27a (Uba80, Ubcep1)
Find proteins for P62983 (Mus musculus)
Go to UniProtKB:  P62983
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF168
E, A
81Homo sapiensMutation(s): 0 
Gene Names: RNF168
EC: 2.3.2.27
Find proteins for Q8IYW5 (Homo sapiens)
Go to Gene View: RNF168
Go to UniProtKB:  Q8IYW5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
H, B
77Mus musculusMutation(s): 0 
Gene Names: Rps27a (Uba80, Ubcep1)
Find proteins for P62983 (Mus musculus)
Go to UniProtKB:  P62983
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PR
Query on PR

Download SDF File 
Download CCD File 
E
PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.220 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.372α = 73.49
b = 50.019β = 69.69
c = 64.407γ = 73.82
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Structure summary
  • Version 1.2: 2018-03-28
    Type: Structure summary