6CVO

Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.

Tumbale, P.Schellenberg, M.J.Mueller, G.A.Fairweather, E.Watson, M.Little, J.N.Krahn, J.Waddell, I.London, R.E.Williams, R.S.

(2018) EMBO J. 37: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aprataxin
A, B
182Homo sapiensMutation(s): 0 
Gene Names: APTX (AXA1)
EC: 3.1.11.7, 3.1.12.2
Find proteins for Q7Z2E3 (Homo sapiens)
Go to Gene View: APTX
Go to UniProtKB:  Q7Z2E3
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3')D,G22Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')E,H6Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.913α = 90.00
b = 72.547β = 90.00
c = 147.164γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NIEHSUnited States1Z01ES102765

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release