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- PDB-4xzh: Crystal structure of human Aldose Reductase complexed with NADP+ ... -

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Basic information

Entry
Database: PDB / ID: 4xzh
TitleCrystal structure of human Aldose Reductase complexed with NADP+ and JF0048
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic
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 / L-ascorbic acid biosynthetic process / prostaglandin H2 endoperoxidase reductase activity / metanephric collecting duct development / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / epithelial cell maturation / retinoid metabolic process / cellular hyperosmotic salinity response / 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. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-48I / 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: 1 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Dominguez, M. / de Lera, A.R. / Farres, J. / Pares, X. / Podjarny, A.
CitationJournal: Chemmedchem / Year: 2015
Title: Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10.
Authors: Ruiz, F.X. / Cousido-Siah, A. / Porte, S. / Dominguez, M. / Crespo, I. / Rechlin, C. / Mitschler, A. / de Lera, A.R. / Martin, M.J. / de la Fuente, J.A. / Klebe, G. / Pares, X. / Farres, J. / Podjarny, A.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Aldose reductase
B: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9636
Polymers71,7972
Non-polymers2,1664
Water14,016778
1
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9813
Polymers35,8981
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9813
Polymers35,8981
Non-polymers1,0832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.485, 46.684, 68.315
Angle α, β, γ (deg.)75.02, 78.93, 74.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


Mass: 35898.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15b / 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


Mass: 743.405 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O17P3
#3: Chemical ChemComp-48I / [3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]acetic acid


Mass: 339.688 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10ClN3O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, ammonium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.7085 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 246041 / % possible obs: 85.9 % / Redundancy: 1.6 % / Rsym value: 0.028 / Net I/σ(I): 22.31
Reflection shellResolution: 1→1.04 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.44 / % possible all: 73.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: dev_1426)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1US0

1us0


Resolution: 1→35.582 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 14.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.161 15366 5.02 %Random 5%
Rwork0.1488 ---
obs0.1494 246041 91.62 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→35.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 46 778 5970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095535
X-RAY DIFFRACTIONf_angle_d1.4467580
X-RAY DIFFRACTIONf_dihedral_angle_d14.0732142
X-RAY DIFFRACTIONf_chiral_restr0.078840
X-RAY DIFFRACTIONf_plane_restr0.009959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.96080.27384730.26529187X-RAY DIFFRACTION87
0.9608-0.97210.26024680.25679323X-RAY DIFFRACTION87
0.9721-0.9840.25664510.2439120X-RAY DIFFRACTION87
0.984-0.99640.23614710.2239213X-RAY DIFFRACTION87
0.9964-1.00950.23735330.21639059X-RAY DIFFRACTION86
1.0095-1.02340.2244510.20689049X-RAY DIFFRACTION85
1.0234-1.0380.21934780.19279080X-RAY DIFFRACTION86
1.038-1.05350.20754450.18558454X-RAY DIFFRACTION80
1.0535-1.06990.17894530.1718704X-RAY DIFFRACTION82
1.0699-1.08750.17915210.15229681X-RAY DIFFRACTION91
1.0875-1.10620.16094890.14529712X-RAY DIFFRACTION91
1.1062-1.12630.16365370.13449711X-RAY DIFFRACTION92
1.1263-1.1480.15014950.12549754X-RAY DIFFRACTION92
1.148-1.17140.13354920.12079832X-RAY DIFFRACTION93
1.1714-1.19690.135060.11759895X-RAY DIFFRACTION93
1.1969-1.22480.135410.1169854X-RAY DIFFRACTION94
1.2248-1.25540.13645310.11519874X-RAY DIFFRACTION94
1.2554-1.28930.12825470.1159966X-RAY DIFFRACTION94
1.2893-1.32730.13375600.11719885X-RAY DIFFRACTION94
1.3273-1.37010.13215160.11269968X-RAY DIFFRACTION94
1.3701-1.41910.13445290.118610059X-RAY DIFFRACTION95
1.4191-1.47590.13955510.118810016X-RAY DIFFRACTION95
1.4759-1.54310.14295160.118610124X-RAY DIFFRACTION95
1.5431-1.62440.13365540.119710013X-RAY DIFFRACTION95
1.6244-1.72620.14325380.129710131X-RAY DIFFRACTION96
1.7262-1.85950.15575540.143110087X-RAY DIFFRACTION95
1.8595-2.04660.14825110.14810166X-RAY DIFFRACTION96
2.0466-2.34270.16595530.153210197X-RAY DIFFRACTION96
2.3427-2.95130.1815450.168910171X-RAY DIFFRACTION96
2.9513-35.60720.16785570.164110338X-RAY DIFFRACTION98

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