1DAF

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID, ADP, AND CALCIUM

Structural Biology Knowledgebase: 1DAF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.172

Literature

Macromolecules
Sequence Display for 1DAF

Classification: LIGASE

Total Structure Weight: 24728.03

Macromolecule Entities
Molecule Chains Length Organism Details
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 3 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)
DSD
Query on DSD

A 7-(CARBOXYAMINO)-8-AMINO-NONANOIC ACID
C10 H20 N2 O4
OQNJZSIPDMTUAJ-JGVFFNPUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.172
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 73.20 α = 90.00
b = 49.20 β = 107.10
c = 61.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1995-05-08
  • Released Date: 1996-06-20
  • Deposition author(s): Huang, W., Jia, J., Schneider, G., Lindqvist, Y.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4