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- PDB-4yvp: Crystal Structure of AKR1C1 complexed with glibenclamide -

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Basic information

Entry
Database: PDB / ID: 4yvp
TitleCrystal Structure of AKR1C1 complexed with glibenclamide
ComponentsAldo-keto reductase family 1 member C1
KeywordsOxidoreductase/Oxidoreductase inhibitor / AKR1C1 inhibitor / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] activity / : / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase ...3-beta-hydroxy-5-beta-steroid dehydrogenase (NADP+) activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase [NAD(P)+] activity / : / steroid dehydrogenase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / indanol dehydrogenase / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity / trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / 3(or 17)alpha-hydroxysteroid dehydrogenase / 3(or 17)beta-hydroxysteroid dehydrogenase / indanol dehydrogenase activity / 3beta(or 20alpha)-hydroxysteroid dehydrogenase / 5-alpha-androstane-3-beta,17-beta-diol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / testosterone dehydrogenase (NADP+) activity / androsterone dehydrogenase [NAD(P)+] activity / ketosteroid monooxygenase activity / intestinal cholesterol absorption / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / 17beta-estradiol 17-dehydrogenase / retinal metabolic process / carboxylic acid binding / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / : / bile acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / bile acid binding / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / Prednisone ADME / prostaglandin metabolic process / bile acid and bile salt transport / 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 / 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
Chem-GBM / 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: 2.6 Å
AuthorsZhao, Y. / Zheng, X. / Zhang, H. / Hu, X.
CitationJournal: Chem.Biol.Interact. / Year: 2015
Title: In vitro inhibition of AKR1Cs by sulphonylureas and the structural basis
Authors: Zhao, Y. / Zheng, X. / Zhang, H. / Zhai, J. / Zhang, L. / Li, C. / Zeng, K. / Chen, Y. / Li, Q. / Hu, X.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Non-polymer description
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
B: Aldo-keto reductase family 1 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1536
Polymers73,6792
Non-polymers2,4754
Water2,450136
1
A: Aldo-keto reductase family 1 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0773
Polymers36,8391
Non-polymers1,2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-6 kcal/mol
Surface area13480 Å2
MethodPISA
2
B: Aldo-keto reductase family 1 member C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0773
Polymers36,8391
Non-polymers1,2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.545, 76.168, 88.706
Angle α, β, γ (deg.)90.00, 94.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldo-keto reductase family 1 member C1 / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Chlordecone reductase homolog HAKRC / ...20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / Chlordecone reductase homolog HAKRC / Dihydrodiol dehydrogenase 1/2 / DD1/DD2 / High-affinity hepatic bile acid-binding protein / HBAB / Indanol dehydrogenase / Trans-1 / 2-dihydrobenzene-1 / 2-diol dehydrogenase


Mass: 36839.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Condon plus)
References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, indanol dehydrogenase, trans-1,2- ...References: UniProt: Q04828, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 20alpha-hydroxysteroid dehydrogenase, indanol dehydrogenase, trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide / Glyburide


Mass: 494.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C23H28ClN3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 23-27% (w/v) PEG 4000, 100 mM Hepes, 10mM CaCl2, 0.4M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 27, 2014 / Details: OXFORD ONYX CCD
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→88.385 Å / Num. all: 20327 / Num. obs: 19305 / % possible obs: 99.81 % / Redundancy: 3.9 % / Rpim(I) all: 0.14 / Rrim(I) all: 0.277 / Net I/σ(I): 5.1 / Num. measured all: 79376
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.6673.90.6670.91142429230.3950.6672.2100
2.74-2.913.90.4861.31102428110.2860.4862.8100
2.91-3.113.90.4081.61029826320.2420.4083.3100
3.11-3.363.90.2892.2962324480.170.2894.3100
3.36-3.683.90.2262.6885022490.1320.2265.7100
3.68-4.113.90.173.4813820700.0990.177.4100
4.11-4.753.90.1285707218030.0750.1288.5100
4.75-5.813.90.1464.2600315360.0850.1467.1100
5.81-8.223.90.1235.3468412130.0730.1237.299.9
8.22-25.3893.50.0717.722606420.0420.07110.195.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTY

3nty


Resolution: 2.6→88.38 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.834 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24724 1006 5 %RANDOM
Rwork0.21159 ---
obs0.21338 19305 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å2-0.66 Å2
2---0.8 Å2-0 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.6→88.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 162 136 5390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195382
X-RAY DIFFRACTIONr_bond_other_d0.0030.025154
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9887312
X-RAY DIFFRACTIONr_angle_other_deg1311880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11624.18244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4681534
X-RAY DIFFRACTIONr_chiral_restr0.0810.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216138
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021226
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0691.8682542
X-RAY DIFFRACTIONr_mcbond_other1.0691.8682541
X-RAY DIFFRACTIONr_mcangle_it1.8532.83174
X-RAY DIFFRACTIONr_mcangle_other1.8532.8013175
X-RAY DIFFRACTIONr_scbond_it1.1181.9312840
X-RAY DIFFRACTIONr_scbond_other1.1181.9322841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9442.8374139
X-RAY DIFFRACTIONr_long_range_B_refined3.60114.5616230
X-RAY DIFFRACTIONr_long_range_B_other3.56914.5666206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 77 -
Rwork0.316 1375 -
obs--100 %

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