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- PDB-4g3j: Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in co... -

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Basic information

Entry
Database: PDB / ID: 4g3j
TitleSterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the VNI derivative (R)-N-(1-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide [R-VNI-triazole (VNT)]
Componentssterol 14-alpha-demethylase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cytochrome P450 fold / heme / monooxygenase / sterol biosynthesis / eukaryotic membrane biogenesis / cytochrome P450 reductase / endoplasmic reticulum membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol metabolic process / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum
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-VNT / Lanosterol 14-alpha-demethylase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsHargrove, T.Y. / Wawrzak, Z. / Waterman, M.R. / Lepesheva, G.I.
CitationJournal: J Infect Dis / Year: 2015
Title: VFV as a New Effective CYP51 Structure-Derived Drug Candidate for Chagas Disease and Visceral Leishmaniasis.
Authors: Lepesheva, G.I. / Hargrove, T.Y. / Rachakonda, G. / Wawrzak, Z. / Pomel, S. / Cojean, S. / Nde, P.N. / Nes, W.D. / Locuson, C.W. / Calcutt, M.W. / Waterman, M.R. / Daniels, J.S. / Loiseau, P.M. / Villalta, F.
History
DepositionJul 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
B: sterol 14-alpha-demethylase
C: sterol 14-alpha-demethylase
D: sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,52712
Polymers203,0404
Non-polymers4,4878
Water12,665703
1
A: sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8823
Polymers50,7601
Non-polymers1,1222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8823
Polymers50,7601
Non-polymers1,1222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8823
Polymers50,7601
Non-polymers1,1222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: sterol 14-alpha-demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8823
Polymers50,7601
Non-polymers1,1222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.013, 79.480, 116.353
Angle α, β, γ (deg.)74.59, 79.28, 68.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
sterol 14-alpha-demethylase / CYP51


Mass: 50759.902 Da / Num. of mol.: 4 / Fragment: UNP residues 29-476 / Mutation: P29G, T30K, D31L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: CYP51, Tb11.02.4080 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q385E8, sterol 14alpha-demethylase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-VNT / N-[(1R)-1-(2,4-dichlorophenyl)-2-(1H-1,2,4-triazol-1-yl)ethyl]-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide


Mass: 505.355 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H18Cl2N6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: potassium phosphate, sodium chloride, glycerol, PEG3350, N-tetradecyl-beta-D-maltoside, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2012 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.82→29.926 Å / Num. all: 162337 / Num. obs: 159091 / % possible obs: 98 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.3
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.4 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G1Q

3g1q


Resolution: 1.83→29.926 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.873 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.275 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22019 8328 5 %RANDOM
Rwork0.16898 ---
obs0.17158 157414 97.11 %-
all-162098 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.19 Å20.31 Å2
2---0.74 Å20.06 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.83→29.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14228 0 312 703 15243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9192.00220232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84851788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00423.252652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.169152596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.55515120
X-RAY DIFFRACTIONr_chiral_restr0.0560.22192
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111332
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.5523.3347164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9884.9898948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8883.7557748
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_restr7.61314912
X-RAY DIFFRACTIONr_sphericity_free21.3775217
X-RAY DIFFRACTIONr_sphericity_bonded13.635515026
LS refinement shellResolution: 1.825→1.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 563 -
Rwork0.22 10693 -
obs--89.62 %

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