5OMF

Closed, ternary structure of KOD DNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 5OMF

Classification: DNA BINDING PROTEIN

Total Structure Weight: 101008.73


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase,DNA polymerase,DNA polymerase A 774 Thermococcus kodakarensis EC#: 2.7.7.7 IUBMB
Mutation: D141A, E143A
Gene Name(s): pol TK0001
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') T 16 Unidentified
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3') P 16 Unidentified

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DTP
Query on DTP

A 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, P GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.195
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 107.91 α = 90.00
b = 147.56 β = 90.00
c = 71.14 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-07-31
  • Released Date: 2017-12-20
  • Deposition author(s): Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.

Revision History

  • Version 1_0: 2017-12-20

    Type: Initial release