3DKP

Human DEAD-box RNA-helicase DDX52, conserved domain I in complex with ADP

Structural Biology Knowledgebase: 3DKP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.182

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DKP

Classification: HYDROLASE

Total Structure Weight: 28403.96

Macromolecule Entities
Molecule Chains Length Organism Details
Probable ATP-dependent RNA helicase DDX52 A 245 Homo sapiens EC#: 3.6.1 IUBMB
Fragment: Conserved domain I: Residues 139-381
Gene Name(s): DDX52 Gene View ROK1 HUSSY-19

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.182
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 40.63 α = 90.00
b = 38.36 β = 90.37
c = 73.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-25
  • Released Date: 2008-08-12
  • Deposition author(s): Lehtio, L., Karlberg, T., Andersson, J., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Olesen, K., Persson, C., Sagemark, J., Thorsell, A.G., Tresaugues, L., van den Berg, S., Welin, M., Wisniewska, M., Wikstrom, M., Schueler, H., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor