4D26

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.225

Literature

Macromolecules
Sequence Display for 4D26

Classification: HYDROLASE

Total Structure Weight: 50551.72


Macromolecule Entities
Molecule Chains Length Organism Details
BMVLG PROTEIN A 434 Bombyx mori Fragment: HELICASE, RESIDUES 135-564
Mutation: E339Q, R342C
Gene Name(s): BmVLG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*GP*AP*CP*AP*UP)-3' D 6 Bombyx mori

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A 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: 2.1 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.225
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 52.96 α = 90.00
b = 77.81 β = 90.00
c = 107.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-05-07
  • Released Date: 2014-06-18
  • Deposition author(s): Spinelli, P., Pillai, R.S., Kadlec, J., Cusack, S.

Revision History

  • Version 1_0: 2014-06-18

    Type: Initial release

  • Version 1_1: 2014-07-02

    Type: Database references