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- PDB-4ck9: STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMP... -

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Basic information

Entry
Database: PDB / ID: 4ck9
TitleSTEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (S)-1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethyl 4- isopropylphenylcarbamate (LFT)
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-LFT / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 31, 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

Downloads & links

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Assembly

Deposited unit
A: STEROL 14-ALPHA DEMETHYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5533
Polymers52,5531
Non-polymers1,0002
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.953, 62.953, 222.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 52552.898 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LFT / (1S)-1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethyl [4-(propan-2-yl)phenyl]carbamate


Mass: 383.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22ClN3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.4 Å3/Da / Density % sol: 49 % / 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: 0.9786
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 30, 2013 / Details: BE LENSES DIAMOND LAUE
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 13383 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % 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 4H6O

4h6o


Resolution: 2.74→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.907 / SU B: 46.233 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.29561 728 5.2 %RANDOM
Rwork0.26902 ---
obs0.27031 13383 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.38 Å20 Å2
2---0.77 Å20 Å2
3---2.48 Å2
Refinement stepCycle: LAST / Resolution: 2.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 70 25 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0193625
X-RAY DIFFRACTIONr_bond_other_d00.023511
X-RAY DIFFRACTIONr_angle_refined_deg0.8571.9944908
X-RAY DIFFRACTIONr_angle_other_deg0.513.0028077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2175431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60923.395162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.32815640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7951528
X-RAY DIFFRACTIONr_chiral_restr0.0510.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02841
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_it5.8785.8221733
X-RAY DIFFRACTIONr_mcbond_other5.8735.8211732
X-RAY DIFFRACTIONr_mcangle_it9.1428.7212161
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0756.3731892
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 60 -
Rwork0.369 925 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5581-0.12990.24520.9238-0.2630.8027-0.40620.0701-0.08860.40020.17380.1074-0.16880.10520.23240.5470.08590.11180.17070.03590.156222.114429.1537241.4569
21.1737-0.10570.28651.3054-0.77050.5012-0.11070.2461-0.08630.4710.0475-0.1153-0.26880.01390.06320.53290.1077-0.02020.2886-0.0790.036422.885732.7915239.5216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 477
2X-RAY DIFFRACTION2A2001 - 2025

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