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 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of ternary complexes of archaeal B-family DNA polymerases.

Kropp, H.M.Betz, K.Wirth, J.Diederichs, K.Marx, A.

(2017) PLoS One 12: e0188005-e0188005

  • DOI: https://doi.org/10.1371/journal.pone.0188005
  • Primary Citation of Related Structures:  
    5OMF, 5OMQ, 5OMV

  • PubMed Abstract: 

    Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.


  • Organizational Affiliation

    Konstanz Research School Chemical Biology, University of Konstanz, Baden-Württemberg, Konstanz, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase,DNA polymerase,DNA polymerase774Thermococcus kodakarensis KOD1Mutation(s): 2 
Gene Names: polTK0001
EC: 2.7.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P77933 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore P77933 
Go to UniProtKB:  P77933
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77933
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')B [auth T]16synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')C [auth P]16synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP (Subject of Investigation/LOI)
Query on DTP

Download Ideal Coordinates CCD File 
M [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
GOL
Query on GOL

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K [auth A],
L [auth A],
N [auth P]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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F [auth A],
G [auth A],
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

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D [auth A],
E [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.909α = 90
b = 147.559β = 90
c = 71.142γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description