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- PDB-8b66: Human Aldose Reductase Mutant A299G in Complex with a Ligand with... -

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Basic information

Entry
Database: PDB / ID: 8b66
TitleHuman Aldose Reductase Mutant A299G in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / human Aldose Reductase / hAR / Aldo-keto-reductase / SAR_061 ligand / nadp+ / diabetes / mutant A299G / closed transient 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 / 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. / 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
Chem-4G7 / CITRIC ACID / 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: 0.95 Å
AuthorsHubert, L.-S. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Aldose Reductase Mutant A299G in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid)
Authors: Hubert, L.-S. / Heine, A. / Klebe, G.
History
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3924
Polymers36,1101
Non-polymers1,2833
Water8,485471
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-5 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 66.881, 49.361
Angle α, β, γ (deg.)90.000, 91.935, 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 Aldo-keto reductase family 1 member B1 / Aldehyde reductase / Aldose reductase / AR


Mass: 36109.543 Da / Num. of mol.: 1 / Mutation: A299G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Plasmid: pET15b / 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-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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-4G7 / 3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid


Mass: 347.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14FNO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 43.17 %
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- ...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-conditions: 120 mM di-ammonium hydrogen citrate pH 5.0, 25% PEG 6000, saturated with inhibitor

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→49.3 Å / Num. obs: 187062 / % possible obs: 96.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 6.34 Å2 / CC1/2: 0.997 / Rsym value: 0.059 / Net I/σ(I): 18.9
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 6.84 / Num. unique obs: 26689 / CC1/2: 0.97 / Rsym value: 0.17 / % possible all: 85.6

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Processing

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

4prr


Resolution: 0.95→39.7 Å / SU ML: 0.0617 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 8.3421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1154 3742 2 %
Rwork0.1052 183310 -
obs0.1054 187052 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.29 Å2
Refinement stepCycle: LAST / Resolution: 0.95→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 83 471 3066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652990
X-RAY DIFFRACTIONf_angle_d1.06814109
X-RAY DIFFRACTIONf_chiral_restr0.0826447
X-RAY DIFFRACTIONf_plane_restr0.0083573
X-RAY DIFFRACTIONf_dihedral_angle_d16.22111160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.1374970.13414753X-RAY DIFFRACTION68.3
0.96-0.970.14631120.12175478X-RAY DIFFRACTION78.28
0.97-0.990.11131310.11156397X-RAY DIFFRACTION91.07
0.99-10.12281410.1056899X-RAY DIFFRACTION99.51
1-1.020.10161410.09866924X-RAY DIFFRACTION99.45
1.02-1.030.11081420.09476979X-RAY DIFFRACTION99.29
1.03-1.050.10591420.0896934X-RAY DIFFRACTION98.97
1.05-1.070.09111390.08526812X-RAY DIFFRACTION97.9
1.07-1.090.09971390.08316828X-RAY DIFFRACTION97.85
1.09-1.110.08631430.0816976X-RAY DIFFRACTION99.64
1.11-1.130.08511410.08066905X-RAY DIFFRACTION99.53
1.13-1.160.09511440.0827059X-RAY DIFFRACTION99.56
1.16-1.180.10821410.08336909X-RAY DIFFRACTION98.99
1.18-1.210.09151390.08426835X-RAY DIFFRACTION97.77
1.21-1.240.10231410.08526883X-RAY DIFFRACTION98.35
1.24-1.280.09331420.0896991X-RAY DIFFRACTION99.66
1.28-1.320.11531420.09256971X-RAY DIFFRACTION99.69
1.32-1.370.10441430.09376960X-RAY DIFFRACTION99.48
1.37-1.420.10621410.09496931X-RAY DIFFRACTION98.94
1.42-1.490.09931390.09466832X-RAY DIFFRACTION97.22
1.49-1.570.0991430.09587006X-RAY DIFFRACTION99.86
1.57-1.670.0871430.0976998X-RAY DIFFRACTION99.92
1.67-1.790.10341430.10626991X-RAY DIFFRACTION99.66
1.79-1.980.13321430.11327002X-RAY DIFFRACTION98.95
1.98-2.260.12141410.11296939X-RAY DIFFRACTION98.76
2.26-2.850.11451440.1247028X-RAY DIFFRACTION99.58
2.85-39.70.1561450.12997090X-RAY DIFFRACTION99.04

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