1OT3

Crystal structure of Drosophila deoxyribonucleotide kinase complexed with the substrate deoxythymidine

Structural Biology Knowledgebase: 1OT3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.227

Literature

Macromolecules
Sequence Display for 1OT3

Classification: TRANSFERASE

Total Structure Weight: 235822.00

Macromolecule Entities
Molecule Chains Length Organism Details
Deoxyribonucleoside Kinase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 250 Drosophila melanogaster EC#: 2.7.1.145 IUBMB
Gene Name(s): dnk CG5452
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE (Synonym)
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F, G, H SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276
  • R-Value Work: 0.227
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.38 α = 90.00
b = 71.16 β = 90.59
c = 226.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-21
  • Released Date: 2003-05-27
  • Deposition author(s): Mikkelsen, N.E., Johansson, K., Karlsson, A., Knecht, W., Andersen, G., Piskur, J., Munch-Petersen, B., Eklund, H.

Revision History

  • 2014-05-28
    Type: Other | Details: data collection date
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4