2RB4

Crystal structure of the Helicase domain of human DDX25 RNA helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.233

Literature

Macromolecules
Sequence Display for 2RB4

Classification: HYDROLASE

Total Structure Weight: 40660.72

Macromolecule Entities
Molecule Chains Length Organism Details
ATP-dependent RNA helicase DDX25 A, B 175 Homo sapiens EC#: 3.6.1 IUBMB
Fragment: Helicase domain: Residues 307-479
Gene Name(s): DDX25 Gene View GRTH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.267
  • R-Value Work: 0.233
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 70.31 α = 90.00
b = 70.31 β = 90.00
c = 187.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-09-18
  • Released Date: 2007-10-02
  • Deposition author(s): Lehtio, L., Hogbom, M., Uppenberg, J., Arrowsmith, C.H., Berglund, H., Edwards, A.M., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)
  • This entry supercedes: 2G2J

Revision History

  • Version 1_0: 2007-10-02

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-10-11

    Type: Data collection