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- PDB-5ajr: Sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in com... -

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Basic information

Entry
Database: PDB / ID: 5ajr
TitleSterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in complex with the 1-tetrazole derivative VT-1161 ((R)-2-(2,4-Difluorophenyl)-1, 1-difluoro-3-(1H-tetrazol-1-yl)-1-(5-(4-(2,2,2-trifluoroethoxy)phenyl) pyridin-2-yl)propan-2-ol)
ComponentsSTEROL 14-ALPHA DEMETHYLASE
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / CYP51 / 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-VT1 / Sterol 14-alpha demethylase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWawrzak, Z. / Hoekstra, W. / I Lepesheva, G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2015
Title: Clinical Candidate Vt-1161'S Antiparasitic Effect in Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme Cyp51 from Trypanosoma Cruzi.
Authors: Hoekstra, W.J. / Hargrove, T.Y. / Wawrzak, Z. / Da Gama Jaen Batista, D. / Da Silva, C.F. / Nefertiti, A.S.G. / Rachakonda, G. / Schotzinger, R.J. / Villalta, F. / Soeiro, M.D.N.C. / Lepesheva, G.I.
History
DepositionFeb 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references / Structure summary
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6973
Polymers52,5531
Non-polymers1,1442
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.060, 63.060, 221.750
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: 29-481
Source method: isolated from a genetically manipulated source
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-VT1 / (R)-2-(2,4-Difluorophenyl)-1,1-difluoro-3-(1H-tetrazol-1-yl)-1-(5-(4-(2,2,2-trifluoroethoxy)phenyl)pyridin-2-yl)propan-2-ol


Mass: 527.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16F7N5O2
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: 47.9 % / 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: Dec 22, 2014 / 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: 2.75→54.61 Å / Num. obs: 14063 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.3
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZG2

3zg2


Resolution: 2.75→54.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.421 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27407 759 5.4 %RANDOM
Rwork0.26559 ---
obs0.26604 13254 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.75→54.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 80 0 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0193765
X-RAY DIFFRACTIONr_bond_other_d0.0020.023630
X-RAY DIFFRACTIONr_angle_refined_deg0.8911.9975106
X-RAY DIFFRACTIONr_angle_other_deg0.5623.0018354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3775447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4923.452168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16115665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9341529
X-RAY DIFFRACTIONr_chiral_restr0.070.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214182
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02869
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_it9.96211.4991794
X-RAY DIFFRACTIONr_mcbond_other9.96511.4971793
X-RAY DIFFRACTIONr_mcangle_it14.89417.2352239
X-RAY DIFFRACTIONr_mcangle_other14.8917.2382240
X-RAY DIFFRACTIONr_scbond_it9.14211.9331970
X-RAY DIFFRACTIONr_scbond_other9.1411.9311971
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.10917.6222867
X-RAY DIFFRACTIONr_long_range_B_refined20.13893.7434820
X-RAY DIFFRACTIONr_long_range_B_other20.13693.744821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 54 -
Rwork0.387 943 -
obs--100 %

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