5JLC

Structure of CYP51 from the pathogen Candida glabrata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal Structures of Full-Length Lanosterol 14 alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery.

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

(2018) Antimicrob Agents Chemother 62

  • DOI: https://doi.org/10.1128/AAC.01134-18
  • Primary Citation of Related Structures:  
    5JLC, 5V5Z

  • PubMed Abstract: 

    Targeting lanosterol 14α-demethylase (LDM) with azole drugs provides prophylaxis and treatments for superficial and disseminated fungal infections, but cure rates are not optimal for immunocompromised patients and individuals with comorbidities. The efficacy of azole drugs has also been reduced due to the emergence of drug-resistant fungal pathogens. We have addressed the need to improve the potency, spectrum, and specificity for azoles by expressing in Saccharomyces cerevisiae functional, recombinant, hexahistidine-tagged, full-length Candida albicans LDM (CaLDM6×His) and Candida glabrata LDM (CgLDM6×His) and determining their X-ray crystal structures. The crystal structures of CaLDM6×His, CgLDM6×His, and ScLDM6×His have the same fold and bind itraconazole in nearly identical conformations. The catalytic domains of the full-length LDMs have the same fold as the CaLDM6×His catalytic domain in complex with posaconazole, with minor structural differences within the ligand binding pocket. Our structures give insight into the LDM reaction mechanism and phenotypes of single-site CaLDM mutations. This study provides a practical basis for the structure-directed discovery of novel antifungals that target LDMs of fungal pathogens.


  • Organizational Affiliation

    Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lanosterol 14-alpha demethylase515Nakaseomyces glabratus CBS 138Mutation(s): 0 
Gene Names: ERG11CYP51CAGL0E04334g
EC: 1.14.13.70 (PDB Primary Data), 1.14.14.154 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P50859 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138))
Explore P50859 
Go to UniProtKB:  P50859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50859
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1YN
Query on 1YN

Download Ideal Coordinates CCD File 
C [auth A]2-[(2R)-butan-2-yl]-4-{4-[4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazin-1-yl]phenyl}-2,4-dihydro-3H-1,2,4-triazol-3-one
C35 H38 Cl2 N8 O4
VHVPQPYKVGDNFY-DFMJLFEVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 237.94α = 90
b = 237.94β = 90
c = 237.94γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health Research Council (HRC)New Zealand--
Marsden FundNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-02-12
    Changes: Database references, Polymer sequence
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description