6U7T

MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.

Woods, R.D.O'Shea, V.L.Chu, A.Cao, S.Richards, J.L.Horvath, M.P.David, S.S.

(2016) Nucleic Acids Res. 44: 801-10


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenine DNA glycosylase
A
366Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mutY
EC: 3.2.2.31
Find proteins for P83847 (Geobacillus stearothermophilus)
Go to UniProtKB:  P83847
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')B11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')C11synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
B
DNA LINKINGC10 H14 N5 O8 PDG
NR1
Query on NR1
C
DNA linkingC5 H13 N O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.800α = 90.00
b = 86.490β = 90.00
c = 140.580γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United States1608934
National Science Foundation (United States)United States1610721

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release