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- PDB-8bjl: Human Aldose Reductase in Complex with a Ligand with a Fluoro-Ind... -

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Basic information

Entry
Database: PDB / ID: 8bjl
TitleHuman Aldose Reductase in Complex with a Ligand with a Fluoro-Indol-Acetic-Acid Structure (Schl44172)
Componentsaldose reductase
KeywordsOXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / Schl44172 ligand / nadp+ / diabetes / closed pocket
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 / renal water homeostasis / retinoid metabolic process / 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
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / 2-(6-fluoranylindol-1-yl)ethanoic acid / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å
AuthorsHubert, L.-S. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Aldose Reductase in Complex with a Ligand with a Fluoro-Indol-Acetic-Acid Structure (Schl44172)
Authors: Hubert, L.-S. / Heine, A. / Klebe, G. / Reul, S. / Schlitzer, M.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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)37,4047
Polymers35,8981
Non-polymers1,5066
Water7,440413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-1 kcal/mol
Surface area12870 Å2
Unit cell
Length a, b, c (Å)47.073, 66.280, 49.342
Angle α, β, γ (deg.)90.000, 92.660, 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 , 6 types, 419 molecules

#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-QXO / 2-(6-fluoranylindol-1-yl)ethanoic acid / 2-(6-fluoro-1H-indol-1-yl)acetic acid


Mass: 193.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8FNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.57 %
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 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000 Soaking: 120 mM ...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 Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000 Soaking: 120 mM Di-Ammoniumhydrogen citrate pH 5, 25% PEG 6000, 50 mM Ligand

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.97→47 Å / Num. obs: 168299 / % possible obs: 93.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 9.98 Å2 / CC1/2: 1 / Rsym value: 0.034 / Net I/σ(I): 23.12
Reflection shellResolution: 0.97→1.03 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 23426 / CC1/2: 0.81 / Rsym value: 0.6 / % possible all: 80.9

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PRR

4prr


Resolution: 0.97→27.09 Å / SU ML: 0.0641 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 11.7432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1256 3364 2 %
Rwork0.1172 164906 -
obs0.1173 168270 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 0.97→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 100 413 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062891
X-RAY DIFFRACTIONf_angle_d0.97713973
X-RAY DIFFRACTIONf_chiral_restr0.0788434
X-RAY DIFFRACTIONf_plane_restr0.0078573
X-RAY DIFFRACTIONf_dihedral_angle_d17.5651124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.2112980.2434807X-RAY DIFFRACTION65.85
0.98-10.25531240.21596082X-RAY DIFFRACTION83.73
1-1.010.1991290.18666328X-RAY DIFFRACTION86.09
1.01-1.030.20221320.16626503X-RAY DIFFRACTION89.1
1.03-1.050.1711380.14886743X-RAY DIFFRACTION91.96
1.05-1.070.14111370.13446748X-RAY DIFFRACTION93.24
1.07-1.090.13471400.12836860X-RAY DIFFRACTION93.61
1.09-1.110.13991410.12356869X-RAY DIFFRACTION93.85
1.11-1.130.12371410.11616909X-RAY DIFFRACTION94.34
1.13-1.160.14071400.10596901X-RAY DIFFRACTION94.46
1.16-1.190.11011420.10556955X-RAY DIFFRACTION94.94
1.19-1.220.11741420.09966943X-RAY DIFFRACTION95.19
1.22-1.260.11171430.10197015X-RAY DIFFRACTION95.72
1.26-1.30.11211440.10227043X-RAY DIFFRACTION95.99
1.3-1.340.11671440.10297055X-RAY DIFFRACTION96.41
1.34-1.40.11671440.10437078X-RAY DIFFRACTION96.9
1.4-1.460.11181460.10447141X-RAY DIFFRACTION97.29
1.46-1.540.10311460.10247170X-RAY DIFFRACTION97.62
1.54-1.630.13771470.10467170X-RAY DIFFRACTION97.87
1.63-1.760.12741470.10847238X-RAY DIFFRACTION98.3
1.76-1.940.12031480.11167237X-RAY DIFFRACTION98.7
1.94-2.220.09991490.11227294X-RAY DIFFRACTION98.96
2.22-2.790.13191500.11887351X-RAY DIFFRACTION99.43
2.79-27.090.12931520.12497466X-RAY DIFFRACTION99.86

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