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- PDB-3s7s: Crystal structure of human placental aromatase complexed with bre... -

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Basic information

Entry
Database: PDB / ID: 3s7s
TitleCrystal structure of human placental aromatase complexed with breast cancer drug exemestane
ComponentsCytochrome P450 19A1
KeywordsOxidoreductase/Oxidoreductase Inhibitor / Cytochrome P450 / Oxidoreductase / Oxidoreductase-Oxidoreductase Inhibitor complex
Function / homology
Function and homology information


aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / negative regulation of macrophage chemotaxis / mammary gland development / steroid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / steroid hydroxylase activity / aromatase activity / female gonad development / uterus development / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
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
Chem-EXM / PROTOPORPHYRIN IX CONTAINING FE / Aromatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsGhosh, D.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Novel aromatase inhibitors by structure-guided design.
Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 19A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8683
Polymers57,9551
Non-polymers9132
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.626, 140.626, 119.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 19A1 / Aromatase / CYPXIX / Cytochrome P-450AROM / Estrogen synthase


Mass: 57954.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP19A1, ARO1, CYAR, CYP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P11511, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EXM / (8alpha,10alpha,13alpha)-6-methylideneandrosta-1,4-diene-3,17-dione / Exemestane, aromasin / Exemestane


Mass: 296.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O2 / Comment: medication, inhibitor*YM

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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: 5.86 Å3/Da / Density % sol: 79.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24-32% PEG 4000, phosphate buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.21→121.79 Å / Num. all: 22611 / Num. obs: 21353 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 106.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23.93
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.21-3.311100
3.31-3.451100
3.45-3.61100
3.6-3.791100
3.79-4.031100
4.03-4.341100
4.34-4.781100
4.78-5.471100
5.47-6.891100
6.89-50199.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→121.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.375 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25569 1148 5.1 %RANDOM
Rwork0.22102 ---
all0.22272 22611 --
obs0.22272 21353 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.385 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å21.39 Å2-0 Å2
2--2.78 Å2-0 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 3.21→121.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3658 0 65 0 3723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223824
X-RAY DIFFRACTIONr_angle_refined_deg1.2272.0125176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0665453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99423.554166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.54615712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4071525
X-RAY DIFFRACTIONr_chiral_restr0.090.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212826
X-RAY DIFFRACTIONr_mcbond_it0.4741.52258
X-RAY DIFFRACTIONr_mcangle_it0.90423672
X-RAY DIFFRACTIONr_scbond_it0.94731566
X-RAY DIFFRACTIONr_scangle_it1.7384.51504
LS refinement shellResolution: 3.21→3.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 89 -
Rwork0.295 1502 -
obs--96.25 %

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