3QXX

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.130

Literature

Macromolecules
Sequence Display for 3QXX

Classification: LIGASE

Total Structure Weight: 28358.60

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 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GDP
Query on GDP

A GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
8AC
Query on 8AC

A 8-aminooctanoic acid
8-aminocaprylic acid (Synonym)
C8 H17 N O2
UQXNEWQGGVUVQA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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)
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: 1.36 Å
  • R-Value Free: 0.162
  • R-Value Work: 0.130
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 81.88 α = 90.00
b = 37.85 β = 101.30
c = 68.84 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): Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2011-03-30

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2012-03-28

    Type: Database references

  • Version 1_3: 2013-03-27

    Type: Database references