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Yorodumi- PDB-1s2a: Crystal structures of prostaglandin D2 11-ketoreductase in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s2a | ||||||
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Title | Crystal structures of prostaglandin D2 11-ketoreductase in complex with the non-steroidal anti-inflammatory drugs flufenamic acid and indomethacin | ||||||
Components | Aldo-keto reductase family 1 member C3 | ||||||
Keywords | OXIDOREDUCTASE / 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 / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process ...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 / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / negative regulation of retinoic acid biosynthetic process / macromolecule metabolic process / 5alpha-androstane-3beta,17beta-diol dehydrogenase activity / Delta4-3-oxosteroid 5beta-reductase activity / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / farnesol catabolic process / geranylgeranyl reductase activity / 3alpha-hydroxysteroid 3-dehydrogenase / : / cellular response to jasmonic acid stimulus / regulation of testosterone biosynthetic process / dihydrotestosterone 17-beta-dehydrogenase activity / androsterone dehydrogenase activity / testosterone biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / RA biosynthesis pathway / cellular response to prostaglandin D stimulus / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / regulation of retinoic acid receptor signaling pathway / retinal metabolic process / testosterone 17-beta-dehydrogenase (NADP+) activity / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / aldo-keto reductase (NADPH) activity / cyclooxygenase pathway / all-trans-retinol dehydrogenase (NAD+) activity / positive regulation of endothelial cell apoptotic process / 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 / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / 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 / response to nutrient / Retinoid metabolism and transport / keratinocyte differentiation / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 1.7 Å | ||||||
Authors | Lovering, A.L. / Ride, J.P. / Bunce, C.M. / Desmond, J.C. / Cummings, S.M. / White, S.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s2a.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s2a.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s2a_validation.pdf.gz | 551.5 KB | Display | wwPDB validaton report |
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Full document | 1s2a_full_validation.pdf.gz | 553.7 KB | Display | |
Data in XML | 1s2a_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1s2a_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/1s2a ftp://data.pdbj.org/pub/pdb/validation_reports/s2/1s2a | HTTPS FTP |
-Related structure data
Related structure data | 1s1pSC 1s1rC 1s2cC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 / |
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#3: Chemical | ChemComp-IMN / |
#4: Chemical | ChemComp-DMS / |
#5: Chemical | ChemComp-UNX / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 33.594 Å / Origin y: -26.535 Å / Origin z: 59.511 Å
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Refinement TLS group |
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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
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