3SUV

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

• PDB DOI: https://doi.org/10.2210/pdb3SUV/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus sp. TS12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-11 Released: 2012-06-06 
• Deposition Author(s): Sumida, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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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 

Starting Model: experimental

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

• PubMed: 22367352 
• DOI: https://doi.org/10.1039/c2ob06636j
• Primary Citation of Related Structures:  
  3SUR, 3SUS, 3SUT, 3SUU, 3SUV, 3SUW


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.87 kDa 
• Atom Count: 4,688 
• Modelled Residue Count: 504 
• Deposited Residue Count: 525 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase	A	525	Paenibacillus sp. TS12	Mutation(s): 0  Gene Names: Hex1 EC: 3.2.1.52
UniProt
Find proteins for D2KW09 (Paenibacillus sp. TS12) Explore D2KW09  Go to UniProtKB:  D2KW09

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOK	C [auth A]	2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN C8 H16 N2 O4 GBRAQQUMMCVTAV-LXGUWJNJSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
NOK	PDBBind:  3SUV	Ki: 2.80e+4 (nM) from 1 assay(s)

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 = 95.553	α = 90
b = 101.993	β = 90
c = 108.09	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Sumida, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description