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- PDB-3hb4: 17beta-hydroxysteroid dehydrogenase type1 complexed with E2B -

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Basic information

Entry
Database: PDB / ID: 3hb4
Title17beta-hydroxysteroid dehydrogenase type1 complexed with E2B
ComponentsEstradiol 17-beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / 17betaHSD1 / Cytoplasm / Lipid synthesis / NADP / Polymorphism / Steroid biosynthesis
Function / homology
Function and homology information


estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
17beta-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E2B / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.21 Å
AuthorsMazumdar, M. / Fournier, D. / Zhu, D.-W. / Cadot, C. / Poirier, D. / Lin, S.-X.
CitationJournal: Biochem.J. / Year: 2009
Title: Binary and ternary crystal structure analyses of a novel inhibitor with 17beta-HSD type 1: a lead compound for breast cancer therapy.
Authors: Mazumdar, M. / Fournier, D. / Zhu, D.W. / Cadot, C. / Poirier, D. / Lin, S.X.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
X: Estradiol 17-beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2932
Polymers34,8881
Non-polymers4061
Water81145
1
X: Estradiol 17-beta-dehydrogenase 1
hetero molecules

X: Estradiol 17-beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5874
Polymers69,7762
Non-polymers8112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5280 Å2
ΔGint-34 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.080, 43.700, 60.510
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Estradiol 17-beta-dehydrogenase 1 / 17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / Placental 17-beta-hydroxysteroid ...17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / Placental 17-beta-hydroxysteroid dehydrogenase / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH


Mass: 34887.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Protein purified from human placenta / Source: (natural) Homo sapiens (human)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-E2B / 3-{[(9beta,14beta,16alpha,17alpha)-3,17-dihydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide


Mass: 405.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.21→18.98 Å / Num. obs: 15658
Reflection shellResolution: 2.21→2.263 Å / Mean I/σ(I) obs: 0.045 / Num. unique all: 14876 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.2.0005refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→18.98 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.818 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25739 782 5 %RANDOM
Rwork0.19079 ---
obs0.19409 14876 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.082 Å
Refinement stepCycle: LAST / Resolution: 2.21→18.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 30 45 2263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222253
X-RAY DIFFRACTIONr_angle_refined_deg2.2352.0013063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71622.28392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96815371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681522
X-RAY DIFFRACTIONr_chiral_restr0.1460.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021686
X-RAY DIFFRACTIONr_nbd_refined0.2310.2977
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.27
X-RAY DIFFRACTIONr_mcbond_it1.3291.51462
X-RAY DIFFRACTIONr_mcangle_it2.15822270
X-RAY DIFFRACTIONr_scbond_it3.263902
X-RAY DIFFRACTIONr_scangle_it4.9724.5793
LS refinement shellResolution: 2.21→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 36 -
Rwork0.206 695 -
obs--100 %

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