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- PDB-5en4: Complex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhi... -

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Basic information

Entry
Database: PDB / ID: 5en4
TitleComplex of 17-beta-hydroxysteroid dehydrogenase type 14 with inhibitor.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / inhibitor complex / steroid dehydrogenase
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-5Q6 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBertoletti, N. / Braun, F. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationKL1204/15-1 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
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 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

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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)29,3554
Polymers28,3431
Non-polymers1,0123
Water1,78399
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)117,42116
Polymers113,3744
Non-polymers4,04712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area18430 Å2
ΔGint-174 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.724, 91.724, 135.022
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-433-

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: 28343.420 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 (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-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-5Q6 / [2,3-bis(oxidanyl)phenyl]-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone


Mass: 325.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FNO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000 20% Hepes 0.1M DMSO 5% / PH range: 7-8

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.52→46.8 Å / Num. obs: 44532 / % possible obs: 99.9 % / Redundancy: 14.6 % / Rsym value: 0.053 / Net I/σ(I): 28.4
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 6.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1492: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDE

1yde


Resolution: 1.52→46.772 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1294 2227 5 %
Rwork0.1079 --
obs0.1089 44529 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→46.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 69 99 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081984
X-RAY DIFFRACTIONf_angle_d1.0622723
X-RAY DIFFRACTIONf_dihedral_angle_d16.6921207
X-RAY DIFFRACTIONf_chiral_restr0.061312
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5198-1.55280.16031370.1092596X-RAY DIFFRACTION99
1.5528-1.58890.12181370.0952604X-RAY DIFFRACTION100
1.5889-1.62870.14011360.09112592X-RAY DIFFRACTION100
1.6287-1.67270.13271380.0882620X-RAY DIFFRACTION100
1.6727-1.72190.13111360.08782592X-RAY DIFFRACTION100
1.7219-1.77750.12591400.08232646X-RAY DIFFRACTION100
1.7775-1.8410.12251370.07652607X-RAY DIFFRACTION100
1.841-1.91480.091380.07782630X-RAY DIFFRACTION100
1.9148-2.00190.11891380.08182616X-RAY DIFFRACTION100
2.0019-2.10750.10881380.08442624X-RAY DIFFRACTION100
2.1075-2.23950.09291390.08872644X-RAY DIFFRACTION100
2.2395-2.41240.12891400.09852648X-RAY DIFFRACTION100
2.4124-2.65510.13511390.11152651X-RAY DIFFRACTION100
2.6551-3.03930.14571420.12322686X-RAY DIFFRACTION100
3.0393-3.82890.15261420.12012702X-RAY DIFFRACTION100
3.8289-46.80.12741500.12622844X-RAY DIFFRACTION100

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