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- PDB-4fia: Crystal Structure of Human CYP46A1 P450 with bicalutamide Bound -

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Basic information

Entry
Database: PDB / ID: 4fia
TitleCrystal Structure of Human CYP46A1 P450 with bicalutamide Bound
ComponentsCholesterol 24-hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP46A1 / bicalutamide complex
Function / homology
Function and homology information


cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / steroid hydroxylase activity / cholesterol catabolic process ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / bile acid biosynthetic process / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / steroid hydroxylase activity / cholesterol catabolic process / regulation of long-term synaptic potentiation / Endogenous sterols / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Cholesterol 24-hydroxylase / Cytochrome P450, E-class, group I / 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
S-bicalutamide / R-BICALUTAMIDE / PROTOPORPHYRIN IX CONTAINING FE / Cholesterol 24-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStout, C.D. / Pikuleva, I.A. / Mast, N.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Binding of a cyano- and fluoro-containing drug bicalutamide to cytochrome P450 46A1: unusual features and spectral response.
Authors: Mast, N. / Zheng, W. / Stout, C.D. / Pikuleva, I.A.
History
DepositionJun 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _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

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Assembly

Deposited unit
A: Cholesterol 24-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6945
Polymers52,1251
Non-polymers1,5694
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.053, 121.053, 142.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cholesterol 24-hydroxylase / CH24H / Cytochrome P450 46A1


Mass: 52125.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46, CYP46A1 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98

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Non-polymers , 5 types, 139 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-0U9 / S-bicalutamide / (2S)-N-[4-cyano-3-(trifluoromethyl)phenyl]-3-[(4-fluorophenyl)sulfonyl]-2-hydroxy-2-methylpropanamide


Mass: 430.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F4N2O4S / Comment: medication, hormone*YM
#4: Chemical ChemComp-198 / R-BICALUTAMIDE / (2R)-N-[4-CYANO-3-(TRIFLUOROMETHYL)PHENYL]-3-[(4-FLUOROPHENYL)SULFONYL]-2-HYDROXY-2-METHYLPROPANAMIDE


Mass: 430.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F4N2O4S / Comment: medication, hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.5 Å3/Da / Density % sol: 50.82 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1→38.821 Å / Num. all: 30829 / Num. obs: 30829 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rsym value: 0.052 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.1-2.215.40.5841.30.584195.8
2.21-2.356.90.3362.30.3361100
2.35-2.516.70.2143.50.2141100
2.51-2.716.60.1475.10.147199.9
2.71-2.976.70.09280.092199.9
2.97-3.326.40.0611.60.06199.9
3.32-3.836.60.04115.80.041199.9
3.83-4.76.30.03219.20.032199.8
4.7-6.646.10.03218.90.032199.7
6.64-38.8215.80.02720.80.027198.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.821 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.229 / SU ML: 0.126 / SU R Cruickshank DPI: 0.0472 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25282 1557 5.1 %RANDOM
Rwork0.20835 ---
obs0.21054 29263 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 107 135 3675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214038
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9716185
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1857.5848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47123.114167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25315645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4111535
X-RAY DIFFRACTIONr_chiral_restr0.110.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214458
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_it0.851.52122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52623428
X-RAY DIFFRACTIONr_scbond_it2.1531492
X-RAY DIFFRACTIONr_scangle_it3.4454.51465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 113 -
Rwork0.173 1916 -
obs--89.9 %

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