5FD0

Streptomyces plicatus N-acetyl-beta-hexosaminidase in complex with NAGlucal

• PDB DOI: https://doi.org/10.2210/pdb5FD0/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces plicatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-15 Released: 2016-10-26 
• Deposition Author(s): Vadlamani, G., Mark, B.L.
• Funding Organization(s): Cystic Fibrosis Canada

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.180 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Literature

N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases.

Santana, A.G., Vadlamani, G., Mark, B.L., Withers, S.G.

(2016) Chem Commun (Camb) 52: 7943-7946

• PubMed: 27253678 
• DOI: https://doi.org/10.1039/c6cc02520j
• Primary Citation of Related Structures:  
  5FCZ, 5FD0


• PubMed Abstract: 
  

  Mono-, di- and trisaccharide derivatives of 1,2-unsaturated N-acetyl-d-glucal have been synthesized and shown to function as tight-binding inhibitors/slow substrates of representative hexosaminidases. Turnover is slow and not observed in the thioamide analogue, allowing determination of the 3-dimensional structure of the complex. Inhibition is insensitive to pH and to mutation of key catalytic residues, consistent with the uncharged character of the inhibitor. These properties could render this inhibitor class less prone to development of resistance.

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Organizational Affiliation: 

Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T1Z3, Canada. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.92 kDa 
• Atom Count: 4,597 
• Modelled Residue Count: 499 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-N-acetylhexosaminidase	A	512	Streptomyces plicatus	Mutation(s): 0  Gene Names: hex
UniProt
Find proteins for O85361 (Streptomyces plicatus) Explore O85361  Go to UniProtKB:  O85361

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NAG	Binding MOAD:  5FD0	Ki: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.180 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.17	α = 90
b = 133.17	β = 90
c = 176.525	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
CrystalClear	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Vadlamani, G., Mark, B.L.

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Funding Organization	Location	Grant Number
Cystic Fibrosis Canada	Canada	--

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary