4NDF

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

Structural Biology Knowledgebase: 4NDF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4NDF

Classification: DNA BINDING PROTEIN / RNA / DNA

Total Structure Weight: 55769.55


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'-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 5 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

E POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.171
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.43 α = 90.00
b = 116.21 β = 90.00
c = 117.14 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