Macromolecules
Sequence Display for 3BER

Classification: HYDROLASE

Total Structure Weight: 28203.31

Macromolecule Entities
Molecule Chains Length Organism Details
Probable ATP-dependent RNA helicase DDX47 A 249 Homo sapiens EC#: 3.6.1 IUBMB
Fragment: Conserved domain I (DEAD): Residues 5-230
Gene Name(s): DDX47 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGE
Query on PGE

A TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.165
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 93.05 α = 90.00
b = 70.37 β = 90.70
c = 35.86 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-20
  • Released Date: 2007-12-04
  • Deposition author(s): Karlberg, T., Busam, R.D., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History

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