Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 63.61 kDa 
• Atom Count: 3899 
• Modelled Residue Count: 434 
• Deposited Residue Count: 555 
• Unique protein chains: 1

5O9Q

Crystal structure of ScGas2 in complex with compound 6

• PDB DOI: 10.2210/pdb5O9Q/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-06-20 Released: 2018-05-02 
• Deposition Author(s): Delso, I., Valero-Gonzalez, J., Gomollon-Bel, F., Castro-Lopez, J., Fang, W., Navratilova, I., Van Aalten, D., Tejero, T., Merino, P., Hurtado-Guerrero, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Literature

Inhibitors against Fungal Cell Wall Remodeling Enzymes.

Delso, I., Valero-Gonzalez, J., Gomollon-Bel, F., Castro-Lopez, J., Fang, W., Navratilova, I., van Aalten, D.M.F., Tejero, T., Merino, P., Hurtado-Guerrero, R.

(2018) ChemMedChem 13: 128-132

• PubMed: 29164827 
• DOI: 10.1002/cmdc.201700720
• Primary Citation of Related Structures:  
  5O9O, 5O9P, 5O9Q, 5O9R, 5O9Y, 5OA2, 5OA6


• PubMed Abstract: 
  

Fungal β-1,3-glucan glucanosyltransferases are glucan-remodeling enzymes that play important roles in cell wall integrity, and are essential for the viability of pathogenic fungi and yeasts. As such, they are considered possible drug targets, although inhibitors of this class of enzymes have not yet been reported. Herein we report a multidisciplinary approach based on a structure-guided design using a highly conserved transglycosylase from Sacharomyces cerevisiae, that leads to carbohydrate derivatives with high affinity for Aspergillus fumigatus Gel4. We demonstrate by X-ray crystallography that the compounds bind in the active site of Gas2/Gel4 and interact with the catalytic machinery. The topological analysis of noncovalent interactions demonstrates that the combination of a triazole with positively charged aromatic moieties are important for optimal interactions with Gas2/Gel4 through unusual pyridinium cation-π and face-to-face π-π interactions. The lead compound is capable of inhibiting AfGel4 with an IC ₅₀ value of 42 μm.

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Organizational Affiliation: 

Fundación ARAID, 50018, Zaragoza, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,3-beta-glucanosyltransferase GAS2	A	555	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: GAS2, YLR343W, L8300.5 EC: 2.4.1
UniProt
Find proteins for Q06135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06135  Go to UniProtKB:  Q06135

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G00024MO GlyCosmos:  G00024MO GlyGen:  G00024MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9PH	C [auth A]	(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[4-(phenylmethoxymethyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol C28 H41 N3 O16 CUNJJKLJJLQYMH-ZJLPYKFYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9PH	Binding MOAD:  5O9Q	Kd: 6200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.963	α = 90
b = 70.508	β = 90
c = 150.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-06-20 
• Released Date: 2018-05-02 
Deposition Author(s): Delso, I., Valero-Gonzalez, J., Gomollon-Bel, F., Castro-Lopez, J., Fang, W., Navratilova, I., Van Aalten, D., Tejero, T., Merino, P., Hurtado-Guerrero, R.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary