4K8X

Binary complex of 9N DNA polymerase in the replicative state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex

Bergen, K.Betz, K.Welte, W.Diederichs, K.Marx, A.

(2013) Chembiochem 14: 1058-1062

  • DOI: 10.1002/cbic.201300175
  • Primary Citation of Related Structures:  4K8Z

  • PubMed Abstract: 
  • Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interacti ...

    Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.


    Organizational Affiliation

    Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
775Thermococcus sp. (strain 9oN-7)Gene Names: pol (polA)
EC: 2.7.7.7
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7))
Go to UniProtKB:  Q56366
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')T16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3')P12N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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T
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
5CY
Query on 5CY

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T
1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-yl}-3,3-dimethyl-3H-indolium
N,N'-(dipropyl)-tetramethylindodicarbocyanine
C31 H39 N2 O2
VFBDPICHYNKCQJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.215α = 90.00
b = 142.616β = 90.00
c = 66.702γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
PHENIXmodel building
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release