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- PDB-1i5r: TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EM1745 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i5r
TitleTYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EM1745 COMPLEX
ComponentsTYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / 17BETA-HYDROXYSTEROID / HYBRID / INHIBITOR
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / 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 / small molecule binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytosol / cytoplasm
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-HYC / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsQiu, W. / Campbell, R.L. / Boivin, P. / Poirier, D. / Lin, S.-X.
CitationJournal: FASEB J. / Year: 2002
Title: A concerted, rational design of type 1 17beta-hydroxysteroid dehydrogenase inhibitors: estradiol-adenosine hybrids with high affinity
Authors: Qiu, W. / Campbell, R.L. / Gangloff, A. / Dupuis, P. / Boivin, R.P. / Tremblay, M.R. / Poirier, D. / Lin, S.X.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 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 / 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
A: TYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8425
Polymers34,8881
Non-polymers9544
Water4,161231
1
A: TYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules

A: TYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,68410
Polymers69,7762
Non-polymers1,9088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9240 Å2
ΔGint-52 kcal/mol
Surface area20390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.272, 42.706, 58.732
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TYPE 1 17 BETA-HYDROXYSTEROID DEHYDROGENASE / ESTRADIOL 17 BETA-DEHYDROGENASE 1 / PLACENTAL 17-BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 34887.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-HYC / O5'-[9-(3,17B-DIHYDROXY-1,3,5(10)-ESTRATRIEN-16B-YL)-NONANOYL]ADENOSINE / EM-1745


Mass: 677.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H51N5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3500, GLYCEROL, SODIUM CHLORIDE, BETA-OCTYL GLUCOSIDE, DITHIOTHREITOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.06 %beta-octylglucoside1drop
216 mg/mlprotein1drop
330 %PEG33501reservoir
4160 mM1reservoirMgCl2
5100 mMTris-HCl1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 1999 / Details: parabolic collimating mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 155176 / Num. obs: 38831 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 26.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3327 / % possible all: 86.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 155176
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 86.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1BHS

1bhs


Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1847 -RANDOM
Rwork0.185 ---
all-38767 --
obs-36941 95.1 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 67 231 2479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.027
X-RAY DIFFRACTIONp_mcangle_it2.209
X-RAY DIFFRACTIONp_mcbond_it1.465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.6-1.6770.2442230.199X-RAY DIFFRACTION4263
1.677-1.7620.2222210.182X-RAY DIFFRACTION4198
1.762-1.8560.1991940.177X-RAY DIFFRACTION3882
1.856-1.9610.211650.169X-RAY DIFFRACTION3480
1.961-2.0780.1981770.17X-RAY DIFFRACTION3080
2.078-2.210.1981570.168X-RAY DIFFRACTION2771
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg20.1
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg0.8

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