3KDE

Crystal structure of the THAP domain from D. melanogaster P-element transposase in complex with its natural DNA binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 3KDE

Classification: DNA BINDING PROTEIN / DNA

Total Structure Weight: 14969.44


Macromolecule Entities
Molecule Chains Length Organism Details
Transposable element P transposase C 77 Drosophila melanogaster Fragment: THAP domain: UNP residues 1-77
Gene Name(s): T Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3' A 10 synthetic 5'-GTTAAG(BRDU)GGA-3'
5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3' B 10 synthetic 5'-(BRDU)CCACTTAAC-3'

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
A, B DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.177
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 28.69 α = 90.00
b = 69.32 β = 92.52
c = 35.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-22
  • Released Date: 2009-12-08
  • Deposition author(s): Sabogal, A., Lyubimov, A.Y., Berger, J.M., Rio, D.C.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2012-02-01
    Type: Other
  • 2012-03-21
    Type: Database references