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- PDB-5o72: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5o72
Title17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal quinoline based inhibitor
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / non-steroidal inhibitor / 17beta-HSD14 / quinoline based inhibitors
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / 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-9MH / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsBertoletti, N. / Braun, F. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationMA-5287/1-1 Germany
German Research FoundationKL-1204/15-1 Germany
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-based design and profiling of novel 17 beta-HSD14 inhibitors.
Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Frotscher, M. / Guragossian, N. / Madeira Girio, P.A. / Le Borgne, M. / Ettouati, L. / Falson, P. / Muller, S. / Vollmer, G. / Heine, ...Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Frotscher, M. / Guragossian, N. / Madeira Girio, P.A. / Le Borgne, M. / Ettouati, L. / Falson, P. / Muller, S. / Vollmer, G. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,7084
Polymers28,6831
Non-polymers1,0263
Water3,657203
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)118,83416
Polymers114,7314
Non-polymers4,10312
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 area21460 Å2
ΔGint-198 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.151, 92.151, 133.191
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-460-

HOH

21A-586-

HOH

31A-602-

HOH

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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-9MH / 2-azanyl-~{N}-[2-(4-fluoranyl-3-oxidanyl-phenyl)carbonylquinolin-7-yl]ethanamide


Mass: 339.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14FN3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 6000 20%, HEPES 0.1 M pH 7.00, DMSO 5% / PH range: 7 - 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 22541 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rsym value: 0.086 / Net I/σ(I): 18.06
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.95 / Num. unique obs: 3581 / Rsym value: 0.493 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4


Resolution: 1.91→46.575 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2127 1126 5 %
Rwork0.1696 --
obs0.1718 22535 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→46.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 70 203 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011968
X-RAY DIFFRACTIONf_angle_d1.0422692
X-RAY DIFFRACTIONf_dihedral_angle_d16.3051192
X-RAY DIFFRACTIONf_chiral_restr0.06313
X-RAY DIFFRACTIONf_plane_restr0.007392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9103-1.99730.26321370.23562617X-RAY DIFFRACTION100
1.9973-2.10260.28391390.21072645X-RAY DIFFRACTION100
2.1026-2.23430.24221370.19632616X-RAY DIFFRACTION99
2.2343-2.40680.2231390.17922635X-RAY DIFFRACTION99
2.4068-2.6490.22471400.17552658X-RAY DIFFRACTION100
2.649-3.03220.20721410.1732682X-RAY DIFFRACTION100
3.0322-3.820.22421420.16042708X-RAY DIFFRACTION100
3.82-46.58840.17011510.14332848X-RAY DIFFRACTION100

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