3PEY

S. cerevisiae Dbp5 bound to RNA and ADP BeF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 3PEY

Classification: HYDROLASE / RNA

Total Structure Weight: 46884.27


Macromolecule Entities
Molecule Chains Length Organism Details
ATP-dependent RNA helicase DBP5 A 395 Saccharomyces cerevisiae EC#: 3.6.4.13 IUBMB
Gene Name(s): DBP5 RAT8 YOR046C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') B 6 synthetic

Small Molecules
Ligands 5 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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEF
Query on BEF

A BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A, B NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
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: 1.4 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.160
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 42.14 α = 90.00
b = 92.21 β = 90.00
c = 104.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-27
  • Released Date: 2011-03-23
  • Deposition author(s): Montpetit, B., Thomsen, N.D., Helmke, K.J., Seeliger, M.A., Berger, J.M., Weis, K.

Revision History

  • 2011-07-13
    Type: Version format compliance