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- PDB-4jq2: AKR1C2 complex with sulindac -

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Basic information

Entry
Database: PDB / ID: 4jq2
TitleAKR1C2 complex with sulindac
ComponentsAldo-keto reductase family 1 member C2
KeywordsOxidoreductase/Oxidoreductase inhibitor / OXIDOREDUCTASE / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


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 / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase 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 / indanol dehydrogenase activity / 3alpha-hydroxysteroid 3-dehydrogenase / phenanthrene 9,10-monooxygenase activity / cellular response to jasmonic acid stimulus / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / androsterone dehydrogenase activity / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)] activity / Oxidoreductases / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / prostaglandin metabolic process / aldose reductase (NADPH) activity / steroid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / Chem-SUZ / L(+)-TARTARIC ACID / Aldo-keto reductase family 1 member C2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYosaatmadja, Y. / Flanagan, J.U. / Squire, C.J.
CitationJournal: To be Published
Title: Structural basis of NSAID selectivity for the aldo-keto reductase 1C family
Authors: Yosaatmadja, Y. / Flanagan, J.U. / Squire, C.J.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member C2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,11312
Polymers75,7152
Non-polymers2,39910
Water5,981332
1
A: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2316
Polymers37,8571
Non-polymers1,3745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo-keto reductase family 1 member C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8826
Polymers37,8571
Non-polymers1,0255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.165, 143.165, 204.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-505-

PO4

21B-505-

PO4

31A-567-

HOH

41B-699-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldo-keto reductase family 1 member C2 / 3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase 2 / DD-2 / DD2 / ...3-alpha-HSD3 / Chlordecone reductase homolog HAKRD / Dihydrodiol dehydrogenase 2 / DD-2 / DD2 / Dihydrodiol dehydrogenase/bile acid-binding protein / DD/BABP / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase / Type III 3-alpha-hydroxysteroid dehydrogenase


Mass: 37857.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C2, DDH2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P52895, Oxidoreductases, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213

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Non-polymers , 6 types, 342 molecules

#2: Chemical ChemComp-SUZ / [(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid / SULINDAC / Sulindac


Mass: 356.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FO3S / Comment: antiinflammatory*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2 M diammonium-L-tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→106.1 Å / Num. all: 80393 / Num. obs: 80393 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 26.1 Å2
Reflection shellResolution: 1.75→1.84 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse unliganded

Resolution: 1.75→19.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.415 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 4023 5 %RANDOM
Rwork0.16307 ---
all0.1661 76267 --
obs0.1661 76267 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.878 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.61 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5051 0 156 332 5539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195431
X-RAY DIFFRACTIONr_bond_other_d0.0020.025195
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9947386
X-RAY DIFFRACTIONr_angle_other_deg0.9413.00311967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64724.057244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57815923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1151533
X-RAY DIFFRACTIONr_chiral_restr0.2160.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021238
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr6.902310626
X-RAY DIFFRACTIONr_sphericity_free22.424595
X-RAY DIFFRACTIONr_sphericity_bonded14.788510730
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 272 -
Rwork0.351 5262 -
obs--92.93 %

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