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- PDB-6tuf: Human Aldose Reductase in complex with ALR43 -

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Basic information

Entry
Database: PDB / ID: 6tuf
TitleHuman Aldose Reductase in complex with ALR43
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 / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NXQ / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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. / Ngo, K.
History
DepositionJan 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)37,2004
Polymers35,8981
Non-polymers1,3023
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-5 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.175, 66.440, 49.219
Angle α, β, γ (deg.)90.000, 92.395, 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/enzymatische-bestimmung-von-saccharose-glucose-nach-din-10326/nadp-dinatriumsalz/p/ae13.1
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
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#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-NXQ / 2-[5-fluoranyl-2-[[3-[methyl(oxidanyl)-$l^{3}-sulfanyl]phenyl]methylcarbamoyl]phenoxy]ethanoic acid


Mass: 366.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17FNO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2017 / Details: Signally 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: 1.15→47.13 Å / Num. obs: 105135 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 10.27 Å2 / CC1/2: 1 / Rsym value: 0.04 / Net I/σ(I): 19.2
Reflection shellResolution: 1.15→1.22 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 16246 / CC1/2: 0.75 / Rsym value: 0.507

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRT

4prt


Resolution: 1.15→34.76 Å / SU ML: 0.0998 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.1643
RfactorNum. reflection% reflection
Rfree0.1524 5257 5 %
Rwork0.1292 --
obs0.1304 105128 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.91 Å2
Refinement stepCycle: LAST / Resolution: 1.15→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 86 375 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062899
X-RAY DIFFRACTIONf_angle_d0.98243988
X-RAY DIFFRACTIONf_chiral_restr0.077437
X-RAY DIFFRACTIONf_plane_restr0.0075565
X-RAY DIFFRACTIONf_dihedral_angle_d15.45571118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.24251470.20712793X-RAY DIFFRACTION83.03
1.16-1.170.23241730.19673293X-RAY DIFFRACTION95.96
1.17-1.190.24651710.22063251X-RAY DIFFRACTION96.02
1.19-1.20.26741720.21983266X-RAY DIFFRACTION95.29
1.2-1.220.21121740.18063311X-RAY DIFFRACTION96.94
1.22-1.240.19641750.16253315X-RAY DIFFRACTION96.46
1.24-1.250.19161730.1663295X-RAY DIFFRACTION97.39
1.25-1.270.20151740.18113291X-RAY DIFFRACTION96.25
1.27-1.290.18931760.15523344X-RAY DIFFRACTION97.97
1.29-1.310.18821730.15183285X-RAY DIFFRACTION96.65
1.31-1.340.18751770.13793359X-RAY DIFFRACTION97.9
1.34-1.360.16971740.13943325X-RAY DIFFRACTION97.66
1.36-1.390.17391750.14873315X-RAY DIFFRACTION97.03
1.39-1.420.18791760.14663354X-RAY DIFFRACTION98.66
1.42-1.450.18521770.13053349X-RAY DIFFRACTION97.73
1.45-1.480.1541760.12093357X-RAY DIFFRACTION97.84
1.48-1.520.14581770.11583350X-RAY DIFFRACTION98.57
1.52-1.560.14211760.11623339X-RAY DIFFRACTION98.16
1.56-1.60.12891770.10563367X-RAY DIFFRACTION97.77
1.6-1.660.12351780.10063393X-RAY DIFFRACTION98.78
1.66-1.710.13051770.10933352X-RAY DIFFRACTION98.82
1.71-1.780.14261780.10563396X-RAY DIFFRACTION99.22
1.78-1.860.13481780.10943379X-RAY DIFFRACTION98.94
1.86-1.960.14251810.11683430X-RAY DIFFRACTION98.88
1.96-2.090.1321770.1173373X-RAY DIFFRACTION98.37
2.09-2.250.1211780.11413384X-RAY DIFFRACTION98.51
2.25-2.470.15571800.12073420X-RAY DIFFRACTION98.96
2.47-2.830.15971730.12513287X-RAY DIFFRACTION96.19
2.83-3.570.15461810.12633430X-RAY DIFFRACTION99.31

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