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- PDB-1s1r: Crystal structures of prostaglandin D2 11-ketoreductase (AKR1C3) ... -

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Basic information

Entry
Database: PDB / ID: 1s1r
TitleCrystal structures of prostaglandin D2 11-ketoreductase (AKR1C3) 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
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member C3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 7, 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)38,8884
Polymers37,9671
Non-polymers9213
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.917, 57.917, 206.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
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
9400 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28450 / Num. obs: 24691 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.092 / Net I/σ(I): 1.7
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 51 Å / Num. obs: 23069 / % possible obs: 94.7 % / Redundancy: 10.6 % / Num. measured all: 243584 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.21 Å / % possible obs: 74.6 % / Redundancy: 1.9 % / Num. unique obs: 2550 / Num. measured obs: 4813 / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IHI

1ihi


Resolution: 2→48.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.639 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1184 4.8 %RANDOM
Rwork0.15774 ---
obs0.15963 23370 100 %-
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: 13.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 52 302 2888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212655
X-RAY DIFFRACTIONr_bond_other_d0.0020.022379
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.993602
X-RAY DIFFRACTIONr_angle_other_deg0.79735564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355315
X-RAY DIFFRACTIONr_chiral_restr0.0730.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02515
X-RAY DIFFRACTIONr_nbd_refined0.1980.2538
X-RAY DIFFRACTIONr_nbd_other0.2310.22808
X-RAY DIFFRACTIONr_nbtor_other0.0810.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.221
X-RAY DIFFRACTIONr_mcbond_it0.4971.51588
X-RAY DIFFRACTIONr_mcangle_it0.95822567
X-RAY DIFFRACTIONr_scbond_it1.5531067
X-RAY DIFFRACTIONr_scangle_it2.6354.51035
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 28
Rwork0.257 665
Refinement TLS params.Method: refined / Origin x: 36.507 Å / Origin y: -20.494 Å / Origin z: 49.263 Å
111213212223313233
T0.0091 Å20.0143 Å2-0.0028 Å2-0.0227 Å2-0.0063 Å2--0.0748 Å2
L0.5242 °20.0321 °20.1646 °2-0.7171 °20.3806 °2--1.0253 °2
S-0.0168 Å °0.027 Å °-0.005 Å °-0.0211 Å °-0.0003 Å °-0.0228 Å °-0.0465 Å °-0.0286 Å °0.0171 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3216 - 321
2X-RAY DIFFRACTION1AC10011
3X-RAY DIFFRACTION1AB - D2001 - 20021
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 51 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.196 / Rfactor Rwork: 0.158
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_deg1.2

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