4TKP

Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activation of the Ubc13-Ub adduct by the RING domain of the TRIM5alpha retroviral restriction factor offers insight into the mechanism of molecular pattern recognition by TRIM proteins

Yudina, Z.Johnson, R.Roa, A.Biris, N.Tsiperson, V.Taylor, A.B.Hart, P.J.Demeler, B.Diaz-Griffero, F.Ivanov, D.N.

(2015) Cell Rep --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
A
153Homo sapiensMutation(s): 0 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tripartite motif-containing protein 5
B
93Macaca mulattaMutation(s): 0 
Gene Names: TRIM5
EC: 2.3.2.27
Find proteins for Q0PF16 (Macaca mulatta)
Go to Gene View: TRIM5
Go to UniProtKB:  Q0PF16
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.170α = 90.00
b = 78.170β = 90.00
c = 82.562γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations, Source and taxonomy