1FYD

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE AMP, ONE PYROPHOSPHATE ION AND ONE MG2+ ION

Structural Biology Knowledgebase: 1FYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1FYD

Classification: LIGASE

Total Structure Weight: 61155.97

Macromolecule Entities
Molecule Chains Length Organism Details
NH(3)-DEPENDENT NAD(+) SYNTHETASE A, B 271 Bacillus subtilis EC#: 6.3.1.5 IUBMB
Gene Name(s): nadE outB BSU03130
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

A PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
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: 2.25 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.191
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.45 α = 90.00
b = 87.20 β = 111.15
c = 61.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-09-28
  • Released Date: 2001-06-06
  • Deposition author(s): Devedjiev, Y., Symersky, J., Singh, R., Brouillette, W., Muccio, D., Jedrzejas, M., Brouillette, C., DeLucas, L.

Revision History

  • 2015-12-30
    Type: Other | Details: Restore position of OXT atom of B1271 that was misplaced during original processing
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4