5YDK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.505 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
E3 ubiquitin-protein ligase RNF168
A, G, F, L
87Homo 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: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
B, H, E, K
76Homo sapiensMutation(s): 1 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
D, J, C, I
77Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.505 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.344α = 90.00
b = 64.120β = 109.62
c = 117.464γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

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