5DPK

MutY adenine glycosylase bound to a transition state analog (1N) paired with d(8-oxoG) in duplexed DNA to 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.242

Literature

Macromolecules
Sequence Display for 5DPK

Classification: HYDROLASE / DNA

Total Structure Weight: 48856.77


Macromolecule Entities
Molecule Chains Length Organism Details
A/G-specific adenine glycosylase A 366 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
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') B 11 Synthetic construct
DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3') C 11 Synthetic construct

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 2 Unique
ID Chains Type Formula 2D Diagram Parent
8OG
Query on 8OG
B DNA LINKING C10 H14 N5 O8 P DG
NR1
Query on NR1
C DNA linking C5 H13 N O5 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.242
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 37.85 α = 90.00
b = 86.62 β = 90.00
c = 140.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-09-12
  • Released Date: 2015-09-23
  • Deposition author(s): Horvath, M.P., O'Shea, V.L., Cao, S., David, S.S.
  • This entry supercedes: 3FSQ

Revision History

  • Version 1_0: 2015-09-23

    Type: Initial release

  • Version 1_1: 2015-12-16

    Type: Database references

  • Version 1_2: 2015-12-30

    Type: Database references

  • Version 1_3: 2016-02-10

    Type: Database references

  • Version 1_4: 2017-09-13

    Type: Author supporting evidence, Database references, Derived calculations