6DTE

GlcNAc-inspired cyclophellitol bound to NagZ

• PDB DOI: https://doi.org/10.2210/pdb6DTE/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia cenocepacia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-15 Released: 2019-04-24 
• Deposition Author(s): Mark, B.L., Winogrodzki, J.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.202 
• R-Value Work: 0.153 
• R-Value Observed: 0.156 

Literature

A mechanism-based GlcNAc-inspired cyclophellitol inactivator of the peptidoglycan recycling enzyme NagZ reverses resistance to beta-lactams in Pseudomonas aeruginosa.

Ho, L.A., Winogrodzki, J.L., Debowski, A.W., Madden, Z., Vocadlo, D.J., Mark, B.L., Stubbs, K.A.

(2018) Chem Commun (Camb) 54: 10630-10633

• PubMed: 30178799 
• DOI: https://doi.org/10.1039/c8cc05281f
• Primary Citation of Related Structures:  
  6DTE


• PubMed Abstract: 
  

  The development of a potent mechanism-based inactivator of NagZ, an enzyme critical to the production of inducible AmpC β-lactamase in Gram-negative bacteria, is presented. This inactivator significantly reduces MIC values for important β-lactams against a clinically relevant strain of Pseudomonas aeruginosa.

---

Organizational Affiliation: 

School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia. [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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.81 kDa 
• Atom Count: 6,028 
• Modelled Residue Count: 679 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase	A, B	350	Burkholderia cenocepacia	Mutation(s): 0  Gene Names: nagZ, A8E72_12990, A8F51_10310, A8F55_30255, BCN122_I0864, BCN122_I2678, BCN122_II1911, UE95_02480 EC: 3.2.1.52
UniProt
Find proteins for A0A125HFC0 (Burkholderia cenocepacia) Explore A0A125HFC0  Go to UniProtKB:  A0A125HFC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H9J	C [auth A], D [auth B]	2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide C9 H14 F3 N O6 RPAYCNWWSJECNN-ZGGPPPIHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.202 
• R-Value Work: 0.153 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.91	α = 90
b = 88.14	β = 92.03
c = 67.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Mark, B.L., Winogrodzki, J.L.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	201603PJT-361930

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description