1K3W

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

Structural Biology Knowledgebase: 1K3W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 1K3W

Classification: HYDROLASE / DNA

Total Structure Weight: 37990.96


Macromolecule Entities
Molecule Chains Length Organism Details
Endonuclease VIII A 262 Escherichia coli EC#: 3.2.2 IUBMB
Mutation: P34T, T112R
Gene Name(s): nei b0714 JW0704
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' B 13 synthetic
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' C 13 synthetic

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

A 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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PED
Query on PED
C NON-POLYMER C5 H13 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.165
  • Space Group: P 43 2 2

Unit Cell:

Length (Å) Angle (°)
a = 76.03 α = 90.00
b = 76.03 β = 90.00
c = 164.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-10-04
  • Released Date: 2002-10-04
  • Deposition author(s): Golan, G., Zharkov, D.O., Gilboa, R., Fernandes, A.S., Kycia, J.H., Gerchman, S.E., Rieger, R.A., Grollman, A.P., Shoham, G.

Revision History

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