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- PDB-1s2a: Crystal structures of prostaglandin D2 11-ketoreductase in comple... -

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Basic information

Entry
Database: PDB / ID: 1s2a
TitleCrystal structures of prostaglandin D2 11-ketoreductase in complex with the non-steroidal anti-inflammatory drugs flufenamic acid and indomethacin
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE / TIM-barrel
Function / homology
Function and homology information


prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase ...prostaglandin-F synthase / testosterone 17beta-dehydrogenase (NADP+) / prostaglandin D2 11-ketoreductase activity / ketoreductase activity / prostaglandin F synthase activity / cellular response to prostaglandin stimulus / cellular response to corticosteroid stimulus / macromolecule metabolic process / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process / 5-alpha-androstane-3-beta,17-beta-diol dehydrogenase (NADP+) activity / Delta4-3-oxosteroid 5beta-reductase activity / farnesol catabolic process / geranylgeranyl reductase activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / prostanoid biosynthetic process / testosterone dehydrogenase (NADP+) activity / androsterone dehydrogenase [NAD(P)+] activity / ketosteroid monooxygenase activity / regulation of testosterone biosynthetic process / RA biosynthesis pathway / testosterone biosynthetic process / : / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / testosterone dehydrogenase (NAD+) activity / regulation of retinoic acid receptor signaling pathway / cellular response to prostaglandin D stimulus / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / retinal metabolic process / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / all-trans-retinol dehydrogenase (NAD+) activity / : / prostaglandin H2 endoperoxidase reductase activity / all-trans-retinol dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / prostaglandin metabolic process / renal absorption / steroid metabolic process / positive regulation of endothelial cell apoptotic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / retinoid metabolic process / Retinoid metabolism and transport / keratinocyte differentiation / response to nutrient / cellular response to calcium ion / cellular response to starvation / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular exosome / nucleus / cytoplasm / 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
INDOMETHACIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 1.7 Å
AuthorsLovering, A.L. / Ride, J.P. / Bunce, C.M. / Desmond, J.C. / Cummings, S.M. / White, S.A.
CitationJournal: Cancer Res. / Year: 2004
Title: Crystal structures of prostaglandin D(2) 11-ketoreductase (AKR1C3) in complex with the nonsteroidal anti-inflammatory drugs flufenamic acid and indomethacin.
Authors: Lovering, A.L. / Ride, J.P. / Bunce, C.M. / Desmond, J.C. / Cummings, S.M. / White, S.A.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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 C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1475
Polymers37,9671
Non-polymers1,1794
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.808, 63.074, 96.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aldo-keto reductase family 1 member C3 / AKR1C3 / prostaglandin D2 11-ketoreductase / Prostaglandin F synthase / 3-alpha-HSD-type-2 / 17- ...AKR1C3 / prostaglandin D2 11-ketoreductase / Prostaglandin F synthase / 3-alpha-HSD-type-2 / 17-beta-HSD-type-5


Mass: 37967.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: P42330, EC: 1.1.1.213, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, 17beta-estradiol 17-dehydrogenase

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-IMN / INDOMETHACIN


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
210 mMpotassium phosphate1droppH7.0
31 mMdithiothreitol1drop
41 mMEDTA1drop
52 mMNADP+1drop
625 %(w/v)PEG40001reservoir
7100 mMsodium citrate1reservoirpH6.0
82.5 %(v/v)MPD1reservoir
9800 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.7→52.7 Å / Num. all: 38057 / Num. obs: 37296 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.54 Å2 / Rsym value: 0.049 / Net I/σ(I): 18.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 5420 / Rsym value: 0.2 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 127566 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 88.3 % / Num. unique obs: 4785 / Num. measured obs: 12797 / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: isomorphous replacement
Starting model: 1S1P

1s1p


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.617 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19838 1860 5 %RANDOM
Rwork0.17227 ---
obs0.17356 35385 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 78 361 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212665
X-RAY DIFFRACTIONr_bond_other_d0.0030.022380
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9983617
X-RAY DIFFRACTIONr_angle_other_deg1.42335560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195314
X-RAY DIFFRACTIONr_chiral_restr0.0760.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022898
X-RAY DIFFRACTIONr_gen_planes_other0.010.02529
X-RAY DIFFRACTIONr_nbd_refined0.2110.2563
X-RAY DIFFRACTIONr_nbd_other0.2320.22916
X-RAY DIFFRACTIONr_nbtor_other0.0860.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2990.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.247
X-RAY DIFFRACTIONr_mcbond_it0.591.51587
X-RAY DIFFRACTIONr_mcangle_it1.1822569
X-RAY DIFFRACTIONr_scbond_it1.93631078
X-RAY DIFFRACTIONr_scangle_it3.2234.51048
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 111
Rwork0.177 2190
Refinement TLS params.Method: refined / Origin x: 33.594 Å / Origin y: -26.535 Å / Origin z: 59.511 Å
111213212223313233
T0.0028 Å2-0.005 Å20.0005 Å2-0.0087 Å2-0.0008 Å2--0.0205 Å2
L0.5453 °20.0235 °20.0792 °2-0.4245 °2-0.4259 °2--0.9809 °2
S0.0265 Å °-0.0126 Å °-0.0196 Å °0.0157 Å °-0.0193 Å °0.0437 Å °0.0281 Å °-0.011 Å °-0.0072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 3207 - 320
2X-RAY DIFFRACTION1AC - D2001 - 20021
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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