3BMX

Beta-N-hexosaminidase (YbbD) from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166
  • R-Value Work: 0.127

Literature

Macromolecules
Sequence Display for 3BMX

Classification: HYDROLASE

Total Structure Weight: 142340.61

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized lipoprotein ybbD A, B 642 Bacillus subtilis EC#: 3.2.1.52 IUBMB
Gene Name(s): nagZ ybbD yzbA BSU01660
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
P4G
Query on P4G

A, B 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166
  • R-Value Work: 0.127
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 58.38 α = 79.79
b = 73.08 β = 69.61
c = 83.57 γ = 88.25

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-13
  • Released Date: 2008-12-16
  • Deposition author(s): Fischer, S.

Revision History

  • Version 1_0: 2008-12-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2014-01-29

    Type: Database references

  • Version 1_3: 2017-10-25

    Type: Advisory, Refinement description