6Q4V

KlenTaq DNA polymerase in complex with dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide.

Kropp, H.M.Diederichs, K.Marx, A.

(2019) Angew.Chem.Int.Ed.Engl. 58: 5457-5461


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I, thermostable
A
541Thermus aquaticusMutation(s): 0 
Gene Names: polA (pol1)
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Go to UniProtKB:  P19821
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(DOC))-3')B12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C16synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DTP
Query on DTP

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Download CCD File 
A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.006 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.482α = 90.00
b = 109.482β = 90.00
c = 91.255γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Database references
  • Version 1.2: 2019-04-10
    Type: Data collection, Database references