1DAM

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP, INORGANIC PHOSPHATE AND MAGNESIUM

Structural Biology Knowledgebase: 1DAM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 1DAM

Classification: LIGASE

Total Structure Weight: 24813.52

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (DETHIOBIOTIN SYNTHETASE) A 224 Escherichia coli EC#: 6.3.3.3 IUBMB
Gene Name(s): bioD1 b0778 JW0761
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTB
Query on DTB

A 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID
D-DESTHIOBIOTIN (Synonym)
C10 H18 N2 O3
AUTOLBMXDDTRRT-JGVFFNPUSA-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)
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: 1.8 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.180
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 72.70 α = 90.00
b = 48.90 β = 106.70
c = 61.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-08-31
  • Released Date: 1999-01-13
  • Deposition author(s): Kaeck, H., Sandmark, J., Gibson, K.J., Schneider, G., Lindqvist, Y.

Revision History

  • 2016-04-06
    Type: Non-polymer description | Details: Update synomym of DTB
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values