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- PDB-3r8g: AKR1C3 complex with ibuprofen -

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Basic information

Entry
Database: PDB / ID: 3r8g
TitleAKR1C3 complex with ibuprofen
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / TIM barrel / ibuprofen / oxidoreductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


prostaglandin D2 11-ketoreductase activity / cellular response to corticosteroid stimulus / regulation of testosterone biosynthetic process / prostaglandin-F synthase / prostaglandin-F synthase activity / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / negative regulation of retinoic acid biosynthetic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / ketoreductase activity ...prostaglandin D2 11-ketoreductase activity / cellular response to corticosteroid stimulus / regulation of testosterone biosynthetic process / prostaglandin-F synthase / prostaglandin-F synthase activity / testosterone 17beta-dehydrogenase (NADP+) / cellular response to prostaglandin stimulus / negative regulation of retinoic acid biosynthetic process / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / ketoreductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / cellular response to prostaglandin D stimulus / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / farnesol catabolic process / macromolecule metabolic process / cellular response to jasmonic acid stimulus / 3alpha-hydroxysteroid 3-dehydrogenase / delta4-3-oxosteroid 5beta-reductase activity / geranylgeranyl reductase activity / phenanthrene 9,10-monooxygenase activity / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / androsterone dehydrogenase activity / RA biosynthesis pathway / testosterone biosynthetic process / retinal metabolic process / regulation of retinoic acid receptor signaling pathway / dihydrotestosterone 17-beta-dehydrogenase activity / ketosteroid monooxygenase activity / steroid dehydrogenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / aldo-keto reductase (NADP) activity / NAD-retinol dehydrogenase activity / cyclooxygenase pathway / positive regulation of endothelial cell apoptotic process / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / bile acid binding / prostaglandin metabolic process / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / renal absorption / 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 / keratinocyte differentiation / cellular response to calcium ion / cellular response to starvation / response to nutrient / positive regulation of cell death / cellular response to cadmium ion / cellular response to reactive oxygen species / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of protein kinase B signaling / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytosol / cytoplasm
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
(2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsYosaatmadja, Y. / Teague, R.M. / Flanagan, J.U. / Squire, C.J.
CitationJournal: Plos One / Year: 2012
Title: Crystal structures of three classes of non-steroidal anti-inflammatory drugs in complex with aldo-keto reductase 1C3.
Authors: Flanagan, J.U. / Yosaatmadja, Y. / Teague, R.M. / Chai, M.Z. / Turnbull, A.P. / Squire, C.J.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9894
Polymers37,9771
Non-polymers1,0123
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.794, 64.533, 96.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aldo-keto reductase family 1 member C3 / 17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha- ...17-beta-hydroxysteroid dehydrogenase type 5 / 17-beta-HSD 5 / 3-alpha-HSD type II / brain / 3-alpha-hydroxysteroid dehydrogenase type 2 / 3-alpha-HSD type 2 / Chlordecone reductase homolog HAKRb / Dihydrodiol dehydrogenase 3 / DD-3 / DD3 / Dihydrodiol dehydrogenase type I / HA1753 / Indanol dehydrogenase / Prostaglandin F synthase / PGFS / Testosterone 17-beta-dehydrogenase 5 / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase


Mass: 37977.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P42330, Oxidoreductases, EC: 1.1.1.213, indanol dehydrogenase, prostaglandin-F synthase, EC: 1.1.1.63, testosterone 17beta-dehydrogenase (NADP+), trans-1,2-dihydrobenzene-1,2-diol 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-IZP / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / (R)-Ibuprofen


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop
Details: 200 mM sodium acetate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 275K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979417 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979417 Å / Relative weight: 1
ReflectionResolution: 1.799→19.73 Å / Num. all: 34038 / Num. obs: 34038 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.3
Reflection shellResolution: 1.799→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4837 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FGB
Resolution: 1.799→19.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.383 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21348 1724 5.1 %RANDOM
Rwork0.17425 ---
all0.17623 32271 --
obs0.17623 32271 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.799→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 67 129 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9983485
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62823.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1371517
X-RAY DIFFRACTIONr_chiral_restr0.1510.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1811.51536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91322480
X-RAY DIFFRACTIONr_scbond_it2.95731023
X-RAY DIFFRACTIONr_scangle_it4.2794.51001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 124 -
Rwork0.273 2289 -
obs--97.65 %
Refinement TLS params.Method: refined / Origin x: 7.19 Å / Origin y: 5.454 Å / Origin z: 10.729 Å
111213212223313233
T0.0317 Å20.0011 Å2-0.0027 Å2-0.0439 Å2-0.0013 Å2--0.0366 Å2
L0.4277 °2-0.0847 °20.0688 °2-0.1495 °2-0.3163 °2--0.7983 °2
S-0.0123 Å °-0.0115 Å °-0.0452 Å °0.0131 Å °-0.0282 Å °-0.0048 Å °-0.0313 Å °0.0012 Å °0.0405 Å °

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