4WMZ | pdb_00004wmz

S. cerevisiae CYP51 complexed with fluconazole in the active site

• PDB DOI: https://doi.org/10.2210/pdb4WMZ/pdb

• Classification: oxidoreductase/oxidoreducatse inhibitor
• Organism(s): Saccharomyces cerevisiae YJM789
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2014-10-09 Released: 2015-07-01 
• Deposition Author(s): Sagatova, A., Keniya, M.V., Wilson, R., Wilbanks, S.M., Monk, B.C., Tyndall, J.D.A.
• Funding Organization(s): Health Research Council (HRC), Marsden Fund

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase.

Sagatova, A.A., Keniya, M.V., Wilson, R.K., Monk, B.C., Tyndall, J.D.

(2015) Antimicrob Agents Chemother 59: 4982-4989

• PubMed: 26055382 
• DOI: https://doi.org/10.1128/AAC.00925-15
• Primary Citation Related Structures: 
  4WMZ


• PubMed Abstract: 
  

  Infections by fungal pathogens such as Candida albicans and Aspergillus fumigatus and their resistance to triazole drugs are major concerns. Fungal lanosterol 14α-demethylase belongs to the CYP51 class in the cytochrome P450 superfamily of enzymes. This monospanning bitopic membrane protein is involved in ergosterol biosynthesis and is the primary target of azole antifungal drugs, including fluconazole. The lack of high-resolution structural information for this drug target from fungal pathogens has been a limiting factor for the design of modified triazole drugs that will overcome resistance. Here we report the X-ray structure of full-length Saccharomyces cerevisiae lanosterol 14α-demethylase in complex with fluconazole at a resolution of 2.05 Å. This structure shows the key interactions involved in fluconazole binding and provides insight into resistance mechanisms by revealing a water-mediated hydrogen bonding network between the drug and tyrosine 140, a residue frequently found mutated to histidine or phenylalanine in resistant clinical isolates.

---

Organizational Affiliation: 
• Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand.
Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin, New Zealand [e-mail] [e-mail].
New Zealand's National School of Pharmacy, University of Otago, Dunedin, New Zealand [e-mail] [e-mail].

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: 62.81 kDa 
• Atom Count: 4,481 
• Modeled Residue Count: 527 
• Deposited Residue Count: 539 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lanosterol 14-alpha demethylase	A	539	Saccharomyces cerevisiae YJM789	Mutation(s): 0  Gene Names: ERG11, SCY_2394 EC: 1.14.14.154 Membrane Entity: Yes
UniProt
Find proteins for A6ZSR0 (Saccharomyces cerevisiae (strain YJM789)) Explore A6ZSR0  Go to UniProtKB:  A6ZSR0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
TPF	C [auth A]	2-(2,4-DIFLUOROPHENYL)-1,3-DI(1H-1,2,4-TRIAZOL-1-YL)PROPAN-2-OL C13 H12 F2 N6 O RFHAOTPXVQNOHP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.24	α = 90
b = 65.21	β = 98.43
c = 81.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Sagatova, A., Keniya, M.V., Wilson, R., Wilbanks, S.M., Monk, B.C., Tyndall, J.D.A.

---

Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	--
Marsden Fund	New Zealand	--

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description