1XNG

Crystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori

Structural Biology Knowledgebase: 1XNG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XNG

Classification: LIGASE

Total Structure Weight: 63146.36

Macromolecule Entities
Molecule Chains Length Organism Details
NH(3)-dependent NAD(+) synthetase A, B 268 Helicobacter pylori EC#: 6.3.1.5 IUBMB
Gene Name(s): nadE HP_0329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINIC ACID ADENINE DINUCLEOTIDE
DEAMIDO-NAD+ (Synonym)
C21 H27 N6 O15 P2
SENPVEZBRZQVST-HISDBWNOSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ATP
Query on ATP

A, B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.229
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.40 α = 90.00
b = 63.40 β = 90.00
c = 125.69 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-05
  • Released Date: 2005-04-05
  • Deposition author(s): Kang, G.B., Kim, Y.S., Im, Y.J., Rho, S.H., Lee, J.H., Eom, S.H.

Revision History

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