6CVQ

Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
180Homo sapiensMutation(s): 1 
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*AP*TP*GP*AP*TP*TP*C)-3')D,G10Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')E,H10Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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

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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: 1.65 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.571α = 90.00
b = 116.049β = 90.00
c = 117.215γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States1Z01ES102765

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references