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- PDB-4qr6: Human Aldose Reductase complexed with a ligand with an IDD struct... -

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Basic information

Entry
Database: PDB / ID: 4qr6
TitleHuman Aldose Reductase complexed with a ligand with an IDD structure (2-[2-(1,3-benzothiazol-2-ylmethylcarbamoyl)-5-fluoro-phenoxy]acetic acid) at 1.05 A
ComponentsAldose reductase
Keywordsoxidoreductase/oxidoreductase inhibitor / TIM BARREL / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / metanephric collecting duct development / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / retinoid metabolic process / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
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 ...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-37V / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRechlin, C. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation
Authors: Rechlin, C. / Scheer, F. / Toth, P. / Heine, A. / Diederich, W. / Klebe, G.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0023
Polymers35,8981
Non-polymers1,1042
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.516, 66.683, 47.350
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / References: UniProt: P15121, aldose reductase
#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-37V / {2-[(1,3-benzothiazol-2-ylmethyl)carbamoyl]-5-fluorophenoxy}acetic acid


Mass: 360.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13FN2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CONTAINS ILE RESIDUES AT THAT POSITION

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.Afterwards the crystals were soaked ...Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5.15 g/L NADP+= 0.66 g/L and Human Aldose Reductase= 15 mg/ml.Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 pH 8.0 saturated with the inhibitor.The well solution was for crystallization was 120mM di-Ammonium hydrogen citrate with 20% PEG6000 pH 5.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2014 / Details: Silicon, active surface 50 nm Rh-coated
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 142734 / Num. obs: 142734 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 7.978 Å2 / Rsym value: 0.043 / Net I/σ(I): 30.1
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 7043 / Rsym value: 0.466 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DUX

2dux


Resolution: 1.05→16.916 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1569 7161 5.02 %random
Rwork0.1405 ---
obs0.1413 142702 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→16.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 73 355 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052699
X-RAY DIFFRACTIONf_angle_d1.2873699
X-RAY DIFFRACTIONf_dihedral_angle_d14.7441005
X-RAY DIFFRACTIONf_chiral_restr0.082412
X-RAY DIFFRACTIONf_plane_restr0.007470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.06190.22532280.20824318X-RAY DIFFRACTION96
1.0619-1.07440.18622440.1864542X-RAY DIFFRACTION100
1.0744-1.08750.18452260.16664424X-RAY DIFFRACTION100
1.0875-1.10130.16852200.15924592X-RAY DIFFRACTION100
1.1013-1.11580.17562450.14634480X-RAY DIFFRACTION100
1.1158-1.1310.1622270.14274547X-RAY DIFFRACTION100
1.131-1.14720.15092390.13374497X-RAY DIFFRACTION100
1.1472-1.16430.14572420.13134482X-RAY DIFFRACTION100
1.1643-1.18250.14372570.13094535X-RAY DIFFRACTION100
1.1825-1.20190.14012660.1324432X-RAY DIFFRACTION100
1.2019-1.22260.16861930.12934552X-RAY DIFFRACTION100
1.2226-1.24480.14322440.12294543X-RAY DIFFRACTION100
1.2448-1.26880.14432380.12214514X-RAY DIFFRACTION100
1.2688-1.29470.13272200.12234543X-RAY DIFFRACTION100
1.2947-1.32280.15832410.12574482X-RAY DIFFRACTION100
1.3228-1.35360.14532280.12264528X-RAY DIFFRACTION100
1.3536-1.38740.16562450.12154533X-RAY DIFFRACTION100
1.3874-1.42490.13352310.11874523X-RAY DIFFRACTION100
1.4249-1.46680.13132350.11834525X-RAY DIFFRACTION100
1.4668-1.51410.12872600.11894507X-RAY DIFFRACTION100
1.5141-1.56820.12892440.12284521X-RAY DIFFRACTION100
1.5682-1.63090.1382380.12614536X-RAY DIFFRACTION100
1.6309-1.70510.14262740.13034496X-RAY DIFFRACTION100
1.7051-1.79490.15852440.13724486X-RAY DIFFRACTION100
1.7949-1.90720.14952490.14084557X-RAY DIFFRACTION100
1.9072-2.05420.15182280.14654559X-RAY DIFFRACTION100
2.0542-2.26050.16962690.1454514X-RAY DIFFRACTION100
2.2605-2.58660.14842270.15934561X-RAY DIFFRACTION100
2.5866-3.25510.18572230.16074576X-RAY DIFFRACTION100
3.2551-16.91850.16742360.14084636X-RAY DIFFRACTION100

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