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- PDB-6zr6: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in compl... -

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Basic information

Entry
Database: PDB / ID: 6zr6
Title17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with non-steroidal inhibitor
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / Inhibitor Complex
Function / homology
Function and homology information


Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
beta-D-glucopyranose / Chem-F45 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBadran, M.J. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with non-steroidal inhibitor
Authors: Badran, M.J. / Heine, A. / Klebe, G.
History
DepositionJul 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5215
Polymers28,3291
Non-polymers1,1924
Water2,936163
1
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,08520
Polymers113,3184
Non-polymers4,76716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area21180 Å2
ΔGint-200 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.102, 91.102, 132.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-563-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family ...17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1


Mass: 28329.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Wild type S205 variant / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 166 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F45 / [6-(3,4-dihydroxyphenyl)pyridin-2-yl](4-fluoro-3-hydroxyphenyl)methanone


Mass: 325.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FNO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG6000 23% w/v HEPES 0.1 M DMSO 2.5% 2-hydroxypropyl-gamma-cyclodextrin 5mM
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 44723 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 18.06 Å2 / CC1/2: 1 / Net I/σ(I): 26
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 7128 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICM

5icm


Resolution: 1.5→46.12 Å / SU ML: 0.1176 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.4319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 2237 5 %
Rwork0.1516 42482 -
obs0.153 44719 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 81 163 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511995
X-RAY DIFFRACTIONf_angle_d0.8152731
X-RAY DIFFRACTIONf_chiral_restr0.0739319
X-RAY DIFFRACTIONf_plane_restr0.0054396
X-RAY DIFFRACTIONf_dihedral_angle_d25.886748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.24721370.16782597X-RAY DIFFRACTION99.31
1.53-1.570.20461390.15932629X-RAY DIFFRACTION99.93
1.57-1.610.1951370.1492606X-RAY DIFFRACTION99.96
1.61-1.650.2071390.14622637X-RAY DIFFRACTION99.96
1.65-1.70.19911360.1362602X-RAY DIFFRACTION100
1.7-1.750.20061390.13372627X-RAY DIFFRACTION100
1.75-1.820.14721380.12862635X-RAY DIFFRACTION99.96
1.82-1.890.16891390.12472637X-RAY DIFFRACTION99.96
1.89-1.980.17461390.13272628X-RAY DIFFRACTION100
1.98-2.080.16161390.13912659X-RAY DIFFRACTION100
2.08-2.210.18851390.13852639X-RAY DIFFRACTION100
2.21-2.380.17621400.14832657X-RAY DIFFRACTION100
2.38-2.620.18031400.15492660X-RAY DIFFRACTION99.89
2.62-30.19391420.16682695X-RAY DIFFRACTION100
3-3.780.16921430.16132720X-RAY DIFFRACTION99.83
3.78-46.120.17561510.15762854X-RAY DIFFRACTION99.87

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