3FHT

Crystal structure of human Dbp5 in complex with AMPPNP and RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 3FHT

Classification: HYDROLASE / RNA

Total Structure Weight: 100708.07


Macromolecule Entities
Molecule Chains Length Organism Details
ATP-dependent RNA helicase DDX19B A, B 412 Homo sapiens EC#: 3.6.4.13 IUBMB
Fragment: Helicase ATP-binding domain, C-terminal domain, residues 68-479
Gene Name(s): DDX19B Gene View DBP5 DDX19 TDBP
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') C, D 10 synthetic

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

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

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

A, B 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: 0.225
  • R-Value Work: 0.168
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 41.60 α = 90.00
b = 79.66 β = 90.02
c = 124.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-12-10
  • Released Date: 2009-02-17
  • Deposition author(s): von Moeller, H., Conti, E.

Revision History

  • Version 1_0: 2009-02-17

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance