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- PDB-3c3u: Crystal structure of AKR1C1 in complex with NADP and 3,5-dichloro... -

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Basic information

Entry
Database: PDB / ID: 3c3u
TitleCrystal structure of AKR1C1 in complex with NADP and 3,5-dichlorosalicylic acid
ComponentsAldo-keto reductase family 1 member C1
KeywordsOXIDOREDUCTASE / Aldo-keto reductase / 20 alpha hydroxysteroid dehydrogenase / AKR1C1 / Cytoplasm / NADP
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 / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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 ...3beta-hydroxy-5beta-steroid dehydrogenase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / 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 / response to organophosphorus / phenanthrene 9,10-monooxygenase activity / 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 / intestinal cholesterol absorption / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)] activity / aldo-keto reductase (NADPH) activity / bile acid metabolic process / bile acid and bile salt transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / Prednisone ADME / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Retinoid metabolism and transport / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / digestion / epithelial cell differentiation / xenobiotic metabolic process / 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. / 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 ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / 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
3,5-dichloro-2-hydroxybenzoic 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 / Resolution: 1.8 Å
AuthorsDhagat, U. / El-Kabbani, O.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Selectivity determinants of inhibitor binding to human 20alpha-hydroxysteroid dehydrogenase: crystal structure of the enzyme in ternary complex with coenzyme and the potent inhibitor 3,5-dichlorosalicylic acid
Authors: Dhagat, U. / Endo, S. / Sumii, R. / Hara, A. / El-Kabbani, O.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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 C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8554
Polymers36,8391
Non-polymers1,0163
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.364, 84.236, 49.183
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 323 / Label seq-ID: 4 - 323

Dom-ID
1
2

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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 / High-affinity hepatic bile acid-binding protein / HBAB / Chlordecone reductase homolog HAKRC / Dihydrodiol dehydrogenase 1/2 / DD1/DD2


Mass: 36839.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1, DDH, DDH1 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): pKKDD1
References: UniProt: Q04828, 20alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical ChemComp-C2U / 3,5-dichloro-2-hydroxybenzoic acid


Mass: 207.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4Cl2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 25% Polyglycol monomethylether 550, 0.01M Zinc sulphate, pH6.5, 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: Dec 13, 2007 / 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: 1.8→30 Å / Num. all: 27340 / Num. obs: 26329 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.99 % / Rmerge(I) obs: 0.0504 / Net I/σ(I): 11.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.2299 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2076 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MRQ

1mrq


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.876 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21761 1316 5 %RANDOM
Rwork0.17446 ---
obs0.17672 26329 96.22 %-
all-27340 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.59 Å2
2--0.92 Å20 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 61 328 2981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222720
X-RAY DIFFRACTIONr_angle_refined_deg1.5642.0023703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6165329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99224.194124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02815474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9791517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022059
X-RAY DIFFRACTIONr_nbd_refined0.1990.21390
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2244
X-RAY DIFFRACTIONr_metal_ion_refined0.0560.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0080.21
X-RAY DIFFRACTIONr_mcbond_it0.9731.51688
X-RAY DIFFRACTIONr_mcangle_it1.37822633
X-RAY DIFFRACTIONr_scbond_it2.32531206
X-RAY DIFFRACTIONr_scangle_it3.3614.51066
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2592 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

TypeWeight position
medium positional0.5
medium thermal2
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 83 -
Rwork0.391 1737 -
obs-1737 83.79 %

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