6G0C

Crystal structure of SdeA catalytic core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination.

Kalayil, S.Bhogaraju, S.Bonn, F.Shin, D.Liu, Y.Gan, N.Basquin, J.Grumati, P.Luo, Z.Q.Dikic, I.

(2018) Nature 557: 734-738


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitinating/deubiquitinating enzyme SdeA
A
695Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)Mutation(s): 0 
Gene Names: sdeA
Find proteins for Q5ZTK4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Go to UniProtKB:  Q5ZTK4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

Download SDF File 
Download CCD File 
A
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.802 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.258 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.721α = 90.00
b = 80.824β = 110.57
c = 86.518γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 1177
ERCGermany742720
German Research FoundationGermanySPP 1580

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references
  • Version 1.2: 2018-06-13
    Type: Data collection, Database references, Structure summary