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- PDB-5l7w: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5l7w
Title17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal inhibitor.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / hydroxysteroid dehydrogenase / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6QU / beta-D-glucopyranose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBertoletti, N. / Braun, F. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationKL-1204/15-1 Germany
German Research FoundationMA-5287/1-1 Germany
CitationJournal: J. Med. Chem. / Year: 2016
Title: First Structure-Activity Relationship of 17 beta-Hydroxysteroid Dehydrogenase Type 14 Nonsteroidal Inhibitors and Crystal Structures in Complex with the Enzyme.
Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Steinmetzer, T. / Salah, M. / Abdelsamie, A.S. / van Koppen, C.J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionJun 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,8935
Polymers28,6831
Non-polymers1,2104
Water3,675204
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)119,57020
Polymers114,7314
Non-polymers4,83916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
Buried area20080 Å2
ΔGint-190 kcal/mol
Surface area32680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.019, 91.019, 132.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

21A-577-

HOH

31A-604-

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: 28682.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / 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, 207 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-6QU / [4-fluoranyl-2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone


Mass: 343.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H11F2NO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000 20% Hepes 0.1 M pH 7.00 DMSO 5% / PH range: 7.00-8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 27439 / % possible obs: 97.6 % / Redundancy: 9.28 % / Rsym value: 0.084 / Net I/σ(I): 17.12
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 8.51 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.65 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4
Resolution: 1.76→39.662 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.71
RfactorNum. reflection% reflection
Rfree0.1905 1372 5 %
Rwork0.1504 --
obs0.1523 27434 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→39.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 82 204 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091990
X-RAY DIFFRACTIONf_angle_d1.0662722
X-RAY DIFFRACTIONf_dihedral_angle_d20.6871185
X-RAY DIFFRACTIONf_chiral_restr0.06316
X-RAY DIFFRACTIONf_plane_restr0.007372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7551-1.81780.25821160.22222209X-RAY DIFFRACTION84
1.8178-1.89060.22191380.19782621X-RAY DIFFRACTION100
1.8906-1.97660.22361380.17882623X-RAY DIFFRACTION100
1.9766-2.08080.24251380.16652628X-RAY DIFFRACTION100
2.0808-2.21120.20631390.15682634X-RAY DIFFRACTION100
2.2112-2.38190.18471390.14932636X-RAY DIFFRACTION100
2.3819-2.62160.18881390.14952636X-RAY DIFFRACTION99
2.6216-3.00080.19291390.14282652X-RAY DIFFRACTION99
3.0008-3.78020.16691410.14042676X-RAY DIFFRACTION99
3.7802-39.67210.17291450.13742747X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1653-0.1041-0.07670.1629-0.09840.18270.0074-0.00020.0886-0.08720.025-0.0017-0.133-0.114500.20080.0124-0.00330.1637-0.00130.1774-4.1932-18.7067-17.3068
20.19310.12410.21390.7271-0.19630.30520.00320.0467-0.0184-0.1340.02030.0148-0.00030.01220.00230.1683-0.0070.00820.1625-0.01090.15410.5103-33.4984-19.5641
30.0262-0.0625-0.02680.22620.09890.7107-0.0186-0.0176-0.0032-0.06640.00790.08490.0295-0.34420.00160.141-0.0185-0.02140.2560.01160.1885-15.9972-33.6103-9.3944
40.1133-0.09950.0790.0812-0.08250.13660.019-0.0305-0.10510.051-0.0349-0.0391-0.0005-0.015-00.1605-0.00450.0010.13550.00870.164-2.4647-31.2641-2.5358
50.0362-0.0334-0.1520.03790.10950.7799-0.0785-0.0073-0.00510.06140.1010.04630.0358-0.0480.00180.3368-0.07810.03350.36750.06220.4024-20.8462-64.12134.6986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 220 )
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 254 )
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 271 )

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