6GZS

Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation.

Pruneda, J.N.Bastidas, R.J.Bertsoulaki, E.Swatek, K.N.Santhanam, B.Clague, M.J.Valdivia, R.H.Urbe, S.Komander, D.

(2018) Nat Microbiol 3: 1377-1384


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deubiquitinase and deneddylase Dub1
A
273Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B)Mutation(s): 0 
Gene Names: cdu1
EC: 3.4.22.-
Find proteins for B0B9A0 (Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B))
Go to UniProtKB:  B0B9A0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B
75Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
B
prop-2-en-1-amine
ALLYLAMINE
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.798α = 90.00
b = 55.768β = 93.57
c = 58.574γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
AutoSolphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomU105192732
European Research CouncilUnited Kingdom724804

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references