5UUF

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.154

Literature

Macromolecules
Sequence Display for 5UUF

Classification: HYDROLASE / DNA / ANTIBIOTIC

Total Structure Weight: 36603.53


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-7-methylguanine glycosylase A 241 Bacillus cereus Gene Name(s): BC_4913
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*CP*CP*AP*(ORP)P*AP*GP*CP*CP*CP*G)-3') B 12 Synthetic construct
DNA (5'-D(*CP*GP*GP*GP*CP*TP*TP*TP*GP*GP*GP*G)-3') C 12 Synthetic construct

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
YTA
Query on YTA

B yatakemycin-adenine nucleobase adduct
C40 H34 N10 O8 S
FJMCEQLVMJYVHU-QGZVFWFLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ORP
Query on ORP
B SACCHARIDE C5 H11 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.191
  • R-Value Work: 0.154
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 39.17 α = 90.00
b = 94.61 β = 111.60
c = 48.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-02-16
  • Released Date: 2017-07-19
  • Deposition author(s): Mullins, E.A., Eichman, B.F.

Revision History

  • Version 1_0: 2017-07-19

    Type: Initial release

  • Version 1_1: 2017-08-16

    Type: Database references

  • Version 1_2: 2017-08-30

    Type: Database references

  • Version 1_3: 2017-09-13

    Type: Author supporting evidence, Refinement description