3FSP

MutY adenine glycosylase bound to a transition state analog (1N) paired with dG in duplexed DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 3FSP

Classification: HYDROLASE / DNA

Total Structure Weight: 49081.95


Macromolecule Entities
Molecule Chains Length Organism Details
A/G-specific adenine glycosylase A 369 Geobacillus stearothermophilus EC#: 3.2.2 IUBMB
Mutation: N144D
Gene Name(s): mutY
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3' B 11 synthetic
5'-D(*T*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3' C 11 synthetic

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 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
NRI
Query on NRI
C DNA LINKING C5 H12 N O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 37.76 α = 90.00
b = 86.14 β = 90.00
c = 140.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-11
  • Released Date: 2010-01-19
  • Deposition author(s): O'Shea, V.L., Horvath, M.P., David, S.S.

Revision History

  • Version 1_0: 2010-01-19

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2017-11-01

    Type: Refinement description