5UUH

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing a fluorinated abasic site (9-mer product complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.141

Literature

Macromolecules
Sequence Display for 5UUH

Classification: HYDROLASE / DNA / ANTIBIOTIC

Total Structure Weight: 34805.45


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(*AP*GP*GP*CP*AP*(ORF)P*AP*GP*C)-3') B 9 Synthetic construct
DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3') C 9 Synthetic construct

Small Molecules
Ligands 2 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)
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
RF5
Query on RF5
B SACCHARIDE C5 H10 F O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.141
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 125.40 α = 90.00
b = 55.75 β = 111.18
c = 48.12 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