1YJ5

Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 1YJ5

Classification: TRANSFERASE

Total Structure Weight: 101849.09

Macromolecule Entities
Molecule Chains Length Organism Details
5' polynucleotide kinase-3' phosphatase catalytic domain A, B 383 Mus musculus EC#: 2.7.1.78 IUBMB
Fragment: residues 140-522
Mutation: M219M, M264M, M465M, M476M, M478M
Gene Name(s): Pnkp
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
5' polynucleotide kinase-3' phosphatase FHA domain C 143 Mus musculus EC#: 2.7.1.78 IUBMB
Fragment: residues 1-143
Gene Name(s): Pnkp

Small Molecules
Ligands 1 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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.219
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 95.47 α = 90.00
b = 169.87 β = 90.00
c = 77.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-13
  • Released Date: 2005-03-15
  • Deposition author(s): Bernstein, N.K., Williams, R.S., Rakovszky, M.L., Cui, D., Green, R., Karimi-Busheri, F., Mani, R.S., Galicia, S., Koch, C.A., Cass, C.E., Durocher, D., Weinfeld, M., Glover, J.N.M.

Revision History

  • Version 1_0: 2005-03-15

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance