5KN9

MutY N-terminal domain in complex with DNA containing an intrahelical oxoG:A base-pair

Structural Biology Knowledgebase: 5KN9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 5KN9

Classification: Hydrolase / DNA

Total Structure Weight: 33256.32


Macromolecule Entities
Molecule Chains Length Organism Details
Adenine DNA glycosylase A 232 Geobacillus stearothermophilus EC#: 3.2.2 IUBMB
Fragment: UNP residues 1-229
Mutation: V51Y, D144N, P164C
Gene Name(s): mutY
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3') C 10 Geobacillus stearothermophilus
DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3') D 10 Geobacillus stearothermophilus

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
C DNA LINKING C10 H14 N5 O8 P DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.169
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 49.88 α = 90.00
b = 38.76 β = 105.66
c = 82.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-27
  • Released Date: 2017-02-08
  • Deposition author(s): Wang, L., Chakravarthy, S., Verdine, G.L.

Revision History

  • 2017-04-05
    Type: Citation | Details: Citation
  • 2017-02-22
    Type: Citation | Details: Citation