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- PDB-8fh8: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -

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Basic information

Entry
Database: PDB / ID: 8fh8
TitleCrystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 Soaked In Hydrogen Peroxide
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / Complex
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / HYDROGEN PEROXIDE / Chem-XY0 / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsArenas, R. / Wilson, D.K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003 Soaked In Hydrogen Peroxide
Authors: Arenas, R. / Wilson, D.K.
History
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,72020
Polymers35,8981
Non-polymers1,82219
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.061, 46.989, 48.237
Angle α, β, γ (deg.)77.105, 66.937, 77.235
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase

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Non-polymers , 5 types, 147 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XY0 / {7-[(5-chloro-1,3-benzothiazol-2-yl)methyl]-8-oxo-7,8-dihydropyrazino[2,3-d]pyridazin-5-yl}acetic acid


Mass: 387.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10ClN5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: H2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3,350, 100 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.96584 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96584 Å / Relative weight: 1
ReflectionResolution: 1.6→36.475 Å / Num. obs: 37282 / % possible obs: 90.5 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.035 / Rrim(I) all: 0.05 / Net I/σ(I): 17.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.216 / Num. unique obs: 1741 / CC1/2: 0.962 / Rpim(I) all: 0.216 / Rrim(I) all: 0.306

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.475 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.166 / SU B: 1.479 / SU ML: 0.052 / Average fsc free: 0.9763 / Average fsc work: 0.9821 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 1845 4.949 %0.05
Rwork0.1666 35436 --
all0.168 ---
obs-37281 90.536 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.543 Å2
Baniso -1Baniso -2Baniso -3
1--1.248 Å20.524 Å20.916 Å2
2---0.164 Å2-1.527 Å2
3---1.561 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 116 128 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122685
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162538
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6563634
X-RAY DIFFRACTIONr_angle_other_deg0.5651.5755852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.393512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.66152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49110455
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.27910114
X-RAY DIFFRACTIONr_chiral_restr0.0910.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.2150.2544
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22389
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21321
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.220
X-RAY DIFFRACTIONr_nbd_other0.1820.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.25
X-RAY DIFFRACTIONr_mcbond_it1.8491.7171259
X-RAY DIFFRACTIONr_mcbond_other1.841.7171259
X-RAY DIFFRACTIONr_mcangle_it2.6493.0861572
X-RAY DIFFRACTIONr_mcangle_other2.6483.0871573
X-RAY DIFFRACTIONr_scbond_it3.072.0461426
X-RAY DIFFRACTIONr_scbond_other3.0692.0461427
X-RAY DIFFRACTIONr_scangle_it4.6043.5932062
X-RAY DIFFRACTIONr_scangle_other4.6043.5932063
X-RAY DIFFRACTIONr_lrange_it5.4420.2073075
X-RAY DIFFRACTIONr_lrange_other5.43920.2033064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6410.191500.19525010.19530150.9670.96987.9270.176
1.641-1.6860.2211350.17925860.18130000.9670.97690.70.163
1.686-1.7350.2121300.17125070.17328960.9710.97991.05660.154
1.735-1.7880.1831130.16323650.16427660.9760.98189.58790.147
1.788-1.8470.21200.16323100.16527340.9770.98388.88080.147
1.847-1.9120.175940.16321340.16326340.9780.98284.58620.149
1.912-1.9840.2161070.15521830.15825170.9740.98590.98130.142
1.984-2.0640.1941180.14921110.15124290.9770.98691.76620.139
2.064-2.1560.1671070.14620460.14723330.9840.98792.28460.138
2.156-2.2610.174840.14419810.14622540.9830.98791.61490.138
2.261-2.3820.1781020.16218240.16321440.9810.98489.83210.156
2.382-2.5260.166960.17316570.17319980.9790.98387.73770.169
2.526-2.70.1961050.16716760.16918850.980.98394.48280.165
2.7-2.9150.219890.16515540.16817510.9740.98393.83210.167
2.915-3.1910.202680.16814450.1716260.9750.98393.05040.174
3.191-3.5640.218450.17812310.17914690.9780.98186.86180.187
3.564-4.1090.181530.16711810.16812970.980.98395.14260.181
4.109-5.0160.191500.1599930.1610980.9830.98894.99090.177
5.016-7.0280.215590.2146920.2148480.980.98388.56130.231
7.028-36.4750.226200.1764590.1784820.9780.98499.37760.198

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