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- PDB-8dl4: S. CEREVISIAE CYP51 COMPLEXED WITH Courmarin-containing INHIBITOR -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8dl4
TitleS. CEREVISIAE CYP51 COMPLEXED WITH Courmarin-containing INHIBITOR
ComponentsLanosterol 14-alpha demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHBITOR / COURMARIN / CYP51 / Sterol Biosynthesis / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHBITOR complex
Function / homology
Function and homology information


ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase activity / methylation / iron ion binding / heme binding / endoplasmic reticulum / membrane
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
beta-D-glucopyranose / PROTOPORPHYRIN IX CONTAINING FE / Chem-SKX / Lanosterol 14-alpha demethylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM789 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsRuma, Y.N. / Keniya, M.V. / Tyndall, J.D. / Monk, B.C.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)19/397 New Zealand
Citation
Journal: To Be Published
Title: S. CEREVISIAE CYP51 COMPLEXED WITH Courmarin-containing INHIBITOR
Authors: Benhamou, R. / Keniya, M.V. / Ruma, Y.N. / Fridman, M. / Tyndall, J.D. / Monk, B.C.
#1: Journal: Antimicrob Agents Chemother / Year: 2015
Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase.
Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D.
History
DepositionJul 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanosterol 14-alpha demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4185
Polymers61,8851
Non-polymers1,5324
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.392, 64.379, 81.003
Angle α, β, γ (deg.)90.000, 98.300, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lanosterol 14-alpha demethylase


Mass: 61885.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM789 (yeast)
Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2DELTA / References: UniProt: A6ZSR0
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 220 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SKX / 7-(diethylamino)-N-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]-2-oxo-2H-1-benzopyran-3-carboxamide


Mass: 497.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25F2N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 44% PEG 400, 0.1 M Glycine, pH 9.5

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Data collection

DiffractionMean temperature: 91 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.91→43.67 Å / Num. obs: 60454 / % possible obs: 99.74 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.38 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0607 / Net I/σ(I): 19.7
Reflection shellResolution: 1.91→1.978 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.408 / Num. unique obs: 5947 / CC1/2: 0.705 / CC star: 0.909 / % possible all: 99.07

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LXJ

4lxj


Resolution: 1.91→43.67 Å / SU ML: 0.2267 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 2008 3.32 %
Rwork0.1914 58401 -
obs0.1921 60409 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.7 Å2
Refinement stepCycle: LAST / Resolution: 1.91→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 107 217 4566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694482
X-RAY DIFFRACTIONf_angle_d0.83856086
X-RAY DIFFRACTIONf_chiral_restr0.0504642
X-RAY DIFFRACTIONf_plane_restr0.0065795
X-RAY DIFFRACTIONf_dihedral_angle_d14.10251678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.34341400.3144053X-RAY DIFFRACTION97.08
1.96-2.010.31541410.28244148X-RAY DIFFRACTION99.91
2.01-2.070.26091380.25364141X-RAY DIFFRACTION99.79
2.07-2.140.26031490.22944170X-RAY DIFFRACTION99.86
2.14-2.210.25371350.21424143X-RAY DIFFRACTION99.79
2.21-2.30.23751520.19744174X-RAY DIFFRACTION99.82
2.3-2.410.19881380.18134159X-RAY DIFFRACTION99.91
2.41-2.530.20451460.1754177X-RAY DIFFRACTION100
2.53-2.690.20471470.17444172X-RAY DIFFRACTION100
2.69-2.90.19411420.18114170X-RAY DIFFRACTION99.93
2.9-3.190.22291410.18114197X-RAY DIFFRACTION99.93
3.19-3.650.21281400.1814198X-RAY DIFFRACTION99.86
3.65-4.60.18591450.17524214X-RAY DIFFRACTION99.66
4.6-43.670.19481540.19524285X-RAY DIFFRACTION99.46

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