3SUV

Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with NHAc-DNJ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation 3D Report Full Report



Literature

Gaining insight into the inhibition of glycoside hydrolase family 20 exo-beta-N-acetylhexosaminidases using a structural approach

Sumida, T.Stubbs, K.A.Ito, M.Yokoyama, S.

(2012) Org Biomol Chem 10: 2607-2612

  • DOI: 10.1039/c2ob06636j
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray struc ...

    One useful methodology that has been used to give insight into how chemically synthesized inhibitors bind to enzymes and the reasons underlying their potency is crystallographic studies of inhibitor-enzyme complexes. Presented here is the X-ray structural analysis of a representative family 20 exo-β-N-acetylhexosaminidase in complex with various known classes of inhibitor of these types of enzymes, which highlights how different inhibitor classes can inhibit the same enzyme. This study will aid in the future development of inhibitors of not only exo-β-N-acetylhexosaminidases but also other types of glycoside hydrolases.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-hexosaminidase
A
525Paenibacillus sp. TS12Mutation(s): 0 
Gene Names: Hex1
EC: 3.2.1.52
Find proteins for D0VX21 (Paenibacillus sp)
Go to UniProtKB:  D0VX21
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOK
Query on NOK

Download CCD File 
A
2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
C8 H16 N2 O4
GBRAQQUMMCVTAV-LXGUWJNJSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NOKKi:  28000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.553α = 90
b = 101.993β = 90
c = 108.09γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release