3QXH

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

Structural Biology Knowledgebase: 3QXH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.142
  • R-Value Work: 0.117

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QXH

Classification: LIGASE

Total Structure Weight: 28188.65

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

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

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

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
Kd: 5800 nM  BindingMOAD
Kd: 5800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.142
  • R-Value Work: 0.117
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.53 α = 90.00
b = 37.97 β = 101.15
c = 68.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-01
  • Released Date: 2011-03-30
  • Deposition author(s): Porebski, P.J., Klimecka, M.M., Chruszcz, M., Murzyn, K., Minor, C., 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