6W4T

APE1 Y269A phosphorothioate substrate complex with abasic DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report



Literature

Characterizing the APE1 DNA Intercalating Loop During DNA Sculpting

Hoitsma, N.M.Whitaker, A.M.Beckwitt, E.C.Jang, S.Agarwal, P.K.Van Houten, B.Freudenthal, B.D.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-(apurinic or apyrimidinic site) lyase
A, B
276Homo sapiensMutation(s): 2 
Gene Names: APEX1APEAPE1APEXAPXHAP1REF1
EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for P27695 (Homo sapiens)
Go to UniProtKB:  P27695
NIH Common Fund Data Resources
PHAROS  P27695
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')C, P21synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')F, V21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.659α = 90
b = 148.315β = 90
c = 153.235γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
Blu-Icedata collection
XDSdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR01 ES029203

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release