2DB3

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

Structural Biology Knowledgebase: 2DB3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 2DB3

Classification: HYDROLASE / RNA

Total Structure Weight: 207551.45


Macromolecule Entities
Molecule Chains Length Organism Details
ATP-dependent RNA helicase vasa A, B, C, D 434 Drosophila melanogaster EC#: 3.6.4.13 IUBMB
Fragment: RESIDUES 200-623
Gene Name(s): vas CG3506
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' E, F, G, H 10 synthetic

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

A, B, C, D PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.197
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.05 α = 90.00
b = 142.33 β = 90.86
c = 130.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-14
  • Released Date: 2006-05-02
  • Deposition author(s): Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4