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- PDB-9fb3: Human Aldose Reductase in Complex with a Covalent Ligand -

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Basic information

Entry
Database: PDB / ID: 9fb3
TitleHuman Aldose Reductase in Complex with a Covalent Ligand
Componentsaldose reductase
KeywordsOXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / covalent fragment / nadp+ / diabetes / covalent binding
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 / all-trans-retinol dehydrogenase (NADP+) activity / metanephric collecting duct development / 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. / 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
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-PG6 / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsKlee, L.-S. / Heine, A. / Glinca, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Aldose Reductase in Complex with a Covalent Ligand
Authors: Klee, L.-S. / Heine, A. / Glinca, S.
History
DepositionMay 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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)37,5159
Polymers35,8981
Non-polymers1,6178
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint12 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.028, 68.070, 49.424
Angle α, β, γ (deg.)90.000, 93.621, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein aldose reductase


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-A1IB0 / ethyl 3-ethanoylbicyclo[1.1.1]pentane-1-carboxylate


Mass: 216.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13ClO3 / Feature type: SUBJECT OF INVESTIGATION
#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-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000 Soaking: SmartSoak(R) from CrystalsFirst

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.33→46.94 Å / Num. obs: 70612 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 25
Reflection shellResolution: 1.33→1.41 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 11283 / CC1/2: 0.89 / Rsym value: 0.548 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→23.68 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.5712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1594 3530 5 %
Rwork0.13 67072 -
obs0.1315 70602 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.33→23.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 99 182 2634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712576
X-RAY DIFFRACTIONf_angle_d1.01983517
X-RAY DIFFRACTIONf_chiral_restr0.075391
X-RAY DIFFRACTIONf_plane_restr0.0068466
X-RAY DIFFRACTIONf_dihedral_angle_d17.6254980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.21151360.17682581X-RAY DIFFRACTION96.9
1.35-1.370.19531400.16712652X-RAY DIFFRACTION100
1.37-1.390.1681400.15522673X-RAY DIFFRACTION100
1.39-1.410.19691420.1492691X-RAY DIFFRACTION99.96
1.41-1.440.19431400.14022667X-RAY DIFFRACTION99.96
1.44-1.460.14731410.132684X-RAY DIFFRACTION100
1.46-1.490.15461400.12282660X-RAY DIFFRACTION100
1.49-1.520.16441420.11752685X-RAY DIFFRACTION100
1.52-1.550.15171410.11522691X-RAY DIFFRACTION99.96
1.55-1.580.14111420.10852695X-RAY DIFFRACTION100
1.58-1.620.1351400.10422659X-RAY DIFFRACTION99.96
1.62-1.660.15461410.10342672X-RAY DIFFRACTION100
1.66-1.70.16861420.1072710X-RAY DIFFRACTION100
1.7-1.750.14141410.10442663X-RAY DIFFRACTION100
1.75-1.810.13421410.10492688X-RAY DIFFRACTION100
1.81-1.870.13741420.10662692X-RAY DIFFRACTION100
1.87-1.950.13951400.1052661X-RAY DIFFRACTION100
1.95-2.040.12381420.10562709X-RAY DIFFRACTION100
2.04-2.150.13011420.10862695X-RAY DIFFRACTION100
2.15-2.280.14451410.10982666X-RAY DIFFRACTION100
2.28-2.460.14421420.11532702X-RAY DIFFRACTION99.96
2.46-2.70.13031420.12652699X-RAY DIFFRACTION100
2.7-3.090.15811420.1332705X-RAY DIFFRACTION99.93
3.09-3.890.18141430.14162713X-RAY DIFFRACTION99.86
3.89-23.680.19481450.16982759X-RAY DIFFRACTION99.86

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