4K8Z

KOD Polymerase in binary complex with dsDNA

Structural Biology Knowledgebase: 4K8Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4K8Z

Classification: TRANSFERASE / DNA

Total Structure Weight: 98925.38


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase A 774 Thermococcus kodakarensis EC#: 2.7.7.7 IUBMB
Mutation: D141A, E143A
Gene Name(s):
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') T 16 synthetic DNA Primer
DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3') P 12 synthetic DNA Template

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

A COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

T MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
2DA
Query on 2DA
P DNA LINKING C10 H14 N5 O5 P DA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.181
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 144.87 α = 90.00
b = 111.78 β = 90.00
c = 67.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-19
  • Released Date: 2013-06-26
  • Deposition author(s): Bergen, K., Betz, K., Welte, W., Diederichs, K., Marx, A.

Revision History

No revisions since initial release