1PU7

Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 3,9-dimethyladenine

Structural Biology Knowledgebase: 1PU7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.183

Literature

Macromolecules
Sequence Display for 1PU7

Classification: HYDROLASE

Total Structure Weight: 50921.21

Macromolecule Entities
Molecule Chains Length Organism Details
3-METHYLADENINE DNA GLYCOSYLASE A, B 218 Helicobacter pylori Mutation: M1V, K102G, K120R, V141A, K205X
Gene Name(s): HP_0602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
39A
Query on 39A

A, B 6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM
3,9-DIMETHYLADENINE (Synonym)
C7 H10 N5
YXTNRNJPEDJTNF-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
39A N/A in BindingDB
Ki: 800000 nM  BindingMOAD
Ki: 800000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.183
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 146.60 α = 90.00
b = 44.40 β = 106.40
c = 81.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-24
  • Released Date: 2003-10-07
  • Deposition author(s): Eichman, B.F., O'Rourke, E.J., Radicella, J.P., Ellenberger, T.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4