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- PDB-3nty: Crystal structure of AKR1C1 in complex with NADP and 5-Phenyl,3-c... -

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Basic information

Entry
Database: PDB / ID: 3nty
TitleCrystal structure of AKR1C1 in complex with NADP and 5-Phenyl,3-chlorosalicylic acid
ComponentsAldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Aldo-keto reductase / 20 alpha hydroxysteroid dehydrogenase / AKR1C1 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / androsterone dehydrogenase (B-specific) activity / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity ...3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / androsterone dehydrogenase (B-specific) activity / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / testosterone dehydrogenase [NAD(P)] activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / response to organophosphorus / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / retinal metabolic process / ketosteroid monooxygenase activity / steroid dehydrogenase activity / intestinal cholesterol absorption / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / bile acid and bile salt transport / carboxylic acid binding / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / aldo-keto reductase (NADP) activity / bile acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / doxorubicin metabolic process / bile acid binding / prostaglandin metabolic process / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / xenobiotic metabolic process / epithelial cell differentiation / digestion / cholesterol homeostasis / positive regulation of reactive oxygen species metabolic process / extracellular exosome / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-chloro-4-hydroxybiphenyl-3-carboxylic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsDhagat, U. / El-Kabbani, O.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Probing the inhibitor selectivity pocket of human 20 alpha-hydroxysteroid dehydrogenase (AKR1C1) with X-ray crystallography and site-directed mutagenesis
Authors: El-Kabbani, O. / Dhagat, U. / Soda, M. / Endo, S. / Matsunaga, T. / Hara, A.
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8974
Polymers36,8391
Non-polymers1,0573
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.607, 84.052, 49.051
Angle α, β, γ (deg.)90.000, 91.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1 member C1 / AKR1C1 / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Trans-1 / 2-dihydrobenzene-1 / 2- ...AKR1C1 / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase / Indanol dehydrogenase / Dihydrodiol dehydrogenase 1/2 / DD1/DD2 / Chlordecone reductase homolog HAKRC / High-affinity hepatic bile acid-binding protein / HBAB


Mass: 36839.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pKK223-3, pKKDD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, trans-1,2-dihydrobenzene-1,2-diol ...References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, indanol dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-5P3 / 5-chloro-4-hydroxybiphenyl-3-carboxylic acid / 5-Phenyl,3-chlorosalicylic acid


Mass: 248.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClO3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 20%v/v Polyethylene glycol monomethyl ether 550, 0.01M Zinc sulphate heptahydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 20, 2010 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 24636 / Num. obs: 22148 / % possible obs: 89.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.37 % / Rmerge(I) obs: 0.0918 / Net I/σ(I): 7.5
Reflection shellResolution: 1.87→1.93 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.3522 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1852 / % possible all: 81.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å28.82 Å
Translation3.5 Å28.82 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C3U
Resolution: 1.87→28.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2564 / WRfactor Rwork: 0.1879 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8109 / SU B: 4.169 / SU ML: 0.123 / SU R Cruickshank DPI: 0.1938 / SU Rfree: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1107 4.9 %RANDOM
Rwork0.185 ---
all0.22 24636 --
obs0.1884 22148 89.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.32 Å2 / Biso mean: 25.3882 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å2-0.83 Å2
2--1.44 Å20 Å2
3----0.49 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.87→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 66 379 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222701
X-RAY DIFFRACTIONr_angle_refined_deg1.8592.0053678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15724.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2171517
X-RAY DIFFRACTIONr_chiral_restr0.1220.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212046
X-RAY DIFFRACTIONr_mcbond_it0.9681.51609
X-RAY DIFFRACTIONr_mcangle_it1.57122611
X-RAY DIFFRACTIONr_scbond_it2.73831092
X-RAY DIFFRACTIONr_scangle_it3.9974.51062
LS refinement shellResolution: 1.87→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 92 -
Rwork0.389 1551 -
all-1627 -
obs-1852 81.1 %

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