4NDH

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

Structural Biology Knowledgebase: 4NDH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4NDH

Classification: DNA BINDING PROTEIN / DNA

Total Structure Weight: 55521.17


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

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

A, B ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.196
  • R-Value Work: 0.162
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.40 α = 90.00
b = 117.08 β = 90.00
c = 118.20 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

  • 2014-02-05
    Type: Citation | Details: Citation update
  • 2014-01-15
    Type: Citation | Details: Citation update