1K3X

Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA

Structural Biology Knowledgebase: 1K3X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.149

Literature

Macromolecules
Sequence Display for 1K3X

Classification: HYDROLASE / DNA

Total Structure Weight: 38810.93


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*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*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 3 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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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 2 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
B DNA LINKING C9 H12 Br N2 O8 P DU
PED
Query on PED
C NON-POLYMER C5 H13 O6 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.149
  • Space Group: P 43 2 2

Unit Cell:

Length (Å) Angle (°)
a = 76.50 α = 90.00
b = 76.50 β = 90.00
c = 164.31 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: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4