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- PDB-4ck8: STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMP... -

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Basic information

Entry
Database: PDB / ID: 4ck8
TitleSTEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl 4-(4-(3,4- dichlorophenyl)piperazin-1-yl)phenylcarbamate (LFD)
ComponentsSTEROL 14-ALPHA DEMETHYLASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / MONOOXYGENASE / STEROL BIOSYNTHESIS / EUKARYOTIC MEMBRANES / CYTOCHROME P450 FOLD / ENDOPLASMIC RETICULUM MEMBRANE
Function / homology
Function and homology information


sterol 14-demethylase activity / sterol biosynthetic process / sterol 14alpha-demethylase / iron ion binding / heme binding / membrane
Similarity search - Function
: / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-LFD / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsFriggeri, L. / Wawrzak, Z. / Tortorella, S. / Lepesheva, G.I.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Basis for Rational Design of Inhibitors Targeting Trypanosoma Cruzi Sterol 14Alpha-Demethylase: Two Regions of the Enzyme Molecule Potentiate its Inhibition.
Authors: Friggeri, L. / Hargrove, T.Y. / Rachakonda, G. / Williams, A.D. / Wawrzak, Z. / Di Santo, R. / De Vita, D. / Waterman, M.R. / Tortorella, S. / Villalta, F. / Lepesheva, G.I.
History
DepositionDec 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROL 14-ALPHA DEMETHYLASE
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5496
Polymers105,1062
Non-polymers2,4444
Water43224
1
A: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7753
Polymers52,5531
Non-polymers1,2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7753
Polymers52,5531
Non-polymers1,2222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 137.180, 152.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein STEROL 14-ALPHA DEMETHYLASE / TC14DM / CYTOCHROME P450 51 / CYP51


Mass: 52552.898 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-481
Source method: isolated from a genetically manipulated source
Details: GENBANK AAW47718.1 / Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: THLAHUEN / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / References: UniProt: Q7Z1V1, sterol 14alpha-demethylase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LFD / (1R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl {4-[4-(3,4-dichlorophenyl)piperazin-1-yl]phenyl}carbamate


Mass: 605.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H25Cl4N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS DESCRIBED IN LEPESHEVA ET AL. (2006) J. BIOL.CHEM., 281, P.3577

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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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2013 / Details: BE LENSES DIAMOND LAUE
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. obs: 36336 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.3
Reflection shellResolution: 2.61→2.67 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZG2

3zg2


Resolution: 2.62→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.895 / SU B: 35.758 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28619 1907 5 %RANDOM
Rwork0.23541 ---
obs0.23793 36336 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--5.51 Å20 Å2
3----5.48 Å2
Refinement stepCycle: LAST / Resolution: 2.62→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7189 0 164 24 7377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197541
X-RAY DIFFRACTIONr_bond_other_d0.0010.027285
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.99710219
X-RAY DIFFRACTIONr_angle_other_deg1.883.00216767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52823.452336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.861151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4581558
X-RAY DIFFRACTIONr_chiral_restr0.0690.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218399
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021745
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.8976.5723592
X-RAY DIFFRACTIONr_mcbond_other6.8726.5713591
X-RAY DIFFRACTIONr_mcangle_it8.0769.8214483
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3147.1793949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.654314826
X-RAY DIFFRACTIONr_sphericity_free17.163515
X-RAY DIFFRACTIONr_sphericity_bonded22.185514647
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 131 -
Rwork0.347 2654 -
obs--99.86 %

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