3RPZ

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.148
  • R-Value Work: 0.134

Literature

Macromolecules
Sequence Display for 3RPZ

Classification: lyase / lyase substrate

Total Structure Weight: 31311.40

Macromolecule Entities
Molecule Chains Length Organism Details
ADP/ATP-dependent NAD(P)H-hydrate dehydratase A 279 Bacillus subtilis EC#: 4.2.1.136 IUBMB
Gene Name(s): nnrD yxkO BSU38720
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE
C21 H32 N7 O18 P3
SZKXTJUOKARGIY-VPHRTNKSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMP
Query on AMP

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
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

Unit Cell:

Length (Å) Angle (°)
a = 91.92 α = 90.00
b = 91.92 β = 90.00
c = 169.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-27
  • Released Date: 2011-07-27
  • Deposition author(s): Shumilin, I.A., Cymborowski, M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2011-07-27

    Type: Initial release

  • Version 1_1: 2011-09-21

    Type: Structure summary

  • Version 1_2: 2013-01-09

    Type: Database references