4NDG

Human Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanadate transition state mimic complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 4NDG

Classification: DNA BINDING PROTEIN / RNA / DNA

Total Structure Weight: 55556.79


Macromolecule Entities
Molecule Chains Length Organism Details
Aprataxin A, B 182 Homo sapiens EC#: 3 IUBMB
Gene Name(s): APTX Gene View AXA1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3' D, G 10 synthetic
5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3' E, H 10 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
V5A
Query on V5A

A, B adenosine-5'-vanadate
C10 H13 N5 O6 V
JVJRKVXEYLCGDR-MSQVLRTGSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 40.28 α = 90.00
b = 114.58 β = 90.00
c = 124.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-26
  • Released Date: 2013-12-18
  • Deposition author(s): Schellenberg, M.J., Tumbale, P.S., Williams, R.S.

Revision History

  • Version 1_0: 2013-12-18

    Type: Initial release

  • Version 1_1: 2014-01-15

    Type: Database references

  • Version 1_2: 2014-02-05

    Type: Database references