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- PDB-6syw: human Aldose Reductase in complex with SAR25 -

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Basic information

Entry
Database: PDB / ID: 6syw
Titlehuman Aldose Reductase in complex with SAR25
Componentsaldose reductase
KeywordsOXIDOREDUCTASE / Diabetes / transient binding pocket / diabetic late effects / polyol pathway / osmotic and oxidative stress / cofactor / NADPH / NADP+ / AKR1B1 / ALDR1 / ALR2
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / 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
CITRIC ACID / Chem-M0K / 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: 0.93 Å
AuthorsSandner, A. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: human Aldose Reductase in complex with SAR25
Authors: Sandner, A. / Heine, A. / Klebe, G. / Diederich, W. / Scheer, F.M.
History
DepositionOct 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1014
Polymers35,8981
Non-polymers1,2033
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-5 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.318, 66.856, 49.286
Angle α, β, γ (deg.)90.000, 91.990, 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

#1: Protein aldose reductase /


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: contains NADP https://www.carlroth.com/de/de/Chemikalien/A-Z-Chemikalien/N/NADP-Dinatriumsalz/NADP-Dinatriumsalz/p/000000050000428a00010023_de
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-M0K / 2-[2-(cyclopropylmethylcarbamoyl)-5-fluoranyl-phenoxy]ethanoic acid


Mass: 267.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14FNO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 6000, DTT, diammonium hydrogen citrate, NADP+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2019 / Details: sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.93→47.29 Å / Num. obs: 181142 / % possible obs: 88.1 % / Redundancy: 4.5 % / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 0.93→0.99 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 19356 / CC1/2: 0.81 / Rsym value: 0.458 / % possible all: 58.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootcoot 0.8.9-premodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRT

4prt


Resolution: 0.93→39.66 Å / Cross valid method: FREE R-VALUE / Details: Phenix Refinement
RfactorNum. reflection% reflection
Rfree0.1229 9058 5 %
Rwork0.1089 --
obs-181133 88.1 %
Refinement stepCycle: LAST / Resolution: 0.93→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 80 463 3024

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