6BOV

Human APE1 substrate complex with an A/G mismatch adjacent the THF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.975 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.

Fairlamb, M.S.Whitaker, A.M.Freudenthal, B.D.

(2018) Acta Crystallogr D Struct Biol 74: 760-768


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-(apurinic or apyrimidinic site) lyase
A, B
318Homo sapiensMutation(s): 3 
Gene Names: APEX1 (APE, APE1, APEX, APX, HAP1, REF1)
EC: 3.1.-.-, 4.2.99.18
Find proteins for P27695 (Homo sapiens)
Go to Gene View: APEX1
Go to UniProtKB:  P27695
Entity ID: 2
MoleculeChainsLengthOrganism
21-mer DNAP21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
21-mer DNAV21synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
P
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.975 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.358α = 83.56
b = 60.371β = 78.43
c = 73.343γ = 88.30
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

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 StatesES024431

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection