6MR8

D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.897 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.

Smith, M.R.Shock, D.D.Beard, W.A.Greenberg, M.M.Freudenthal, B.D.Wilson, S.H.

(2019) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A
335Homo sapiensMutation(s): 1 
Gene Names: POLB
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06746 (Homo sapiens)
Go to Gene View: POLB
Go to UniProtKB:  P06746
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')T16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')P10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*GP*G)-3')D5synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GKS
Query on GKS

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A
1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol
C11 H19 N4 O14 P3
SEYTZONDTLWHRH-APQOSEDMSA-N
 Ligand Interaction
NA
Query on NA

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A, T
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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P
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.897 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.015α = 90.00
b = 80.282β = 110.46
c = 55.564γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesES027558

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release