3QXS

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ANP

Structural Biology Knowledgebase: 3QXS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.143

Literature

Macromolecules
Sequence Display for 3QXS

Classification: LIGASE

Total Structure Weight: 28423.52

Macromolecule Entities
Molecule Chains Length Organism Details
Dethiobiotin synthetase A 242 Helicobacter pylori EC#: 6.3.3.3 IUBMB
Gene Name(s): bioD HP_0029
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ANP
Query on ANP

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.143
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.08 α = 90.00
b = 37.58 β = 101.28
c = 69.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-02
  • Released Date: 2011-03-30
  • Deposition author(s): Klimecka, M.M., Porebski, P.J., Chruszcz, M., Jablonska, K., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update
  • 2012-03-28
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4