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- PDB-2f38: Crystal structure of prostaglandin F synathase containing bimatoprost -

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Basic information

Entry
Database: PDB / ID: 2f38
TitleCrystal structure of prostaglandin F synathase containing bimatoprost
ComponentsAldo-keto reductase family 1 member C3
KeywordsOXIDOREDUCTASE / Prostaglandin F synthase / AKR1C3 / PGF2alpha fromation / PGH2 / bimatoprost / catalytic mechanism
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
Chem-15M / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKomoto, J. / Yamada, T. / Watanabe, K. / Woodward, D.F. / Takusagawa, F.
CitationJournal: Biochemistry / Year: 2006
Title: Prostaglandin F2alpha formation from prostaglandin H2 by prostaglandin F synthase (PGFS): crystal structure of PGFS containing bimatoprost.
Authors: Komoto, J. / Yamada, T. / Watanabe, K. / Woodward, D.F. / Takusagawa, F.
History
DepositionNov 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0553
Polymers36,8961
Non-polymers1,1592
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.27, 78.16, 48.89
Angle α, β, γ (deg.)90.0, 100.2, 90.0
Int Tables number4
Space group name H-MP1211
DetailsMonomeric protein containing one NADPH and one bimatoprost.

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Components

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


Mass: 36896.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C3, DDH1, KIAA0119, PGFS / Plasmid: pUC-hLuFS / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P42330, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase, EC: 1.1.1.213, prostaglandin-F synthase, 17beta-estradiol 17-dehydrogenase
#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-15M / (5Z)-7-{(1R,2R,3R,5S)-3,5-DIHYDROXY-2-[(1E,3S)-3-HYDROXY-5-PHENYLPENT-1-ENYL]CYCLOPENTYL}-N-ETHYLHEPT-5-ENAMIDE / BIMATOPROST


Mass: 415.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H37NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 mM BMP, 1.0 mM NADPH, 0.14 M NaCl, 50 mM MES, 26% PEG-8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 19525 / Num. obs: 19525 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 63

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RY0

1ry0


Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 1923 RANDOM
Rwork0.22 --
all0.221 17602 -
obs0.221 17602 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 78 115 2756

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