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- PDB-8fh5: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -

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Basic information

Entry
Database: PDB / ID: 8fh5
TitleCrystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-001
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / COMPLEX / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / OXIDOREDUCTASE
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 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-XXQ / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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-001
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)36,9323
Polymers35,7671
Non-polymers1,1652
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.144, 47.026, 47.340
Angle α, β, γ (deg.)75.871, 67.434, 76.779
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35767.145 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
#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-XXQ / (8-oxo-7-{[5-(trifluoromethyl)-1,3-benzothiazol-2-yl]methyl}-7,8-dihydropyrazino[2,3-d]pyridazin-5-yl)acetic acid


Mass: 421.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10F3N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3350, 100 mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.62→36.674 Å / Num. obs: 34509 / % possible obs: 88.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.059 / Net I/σ(I): 16.7
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.145 / Num. unique obs: 1727 / CC1/2: 0.976 / Rpim(I) all: 0.145 / Rrim(I) all: 0.205

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→36.674 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.146 / SU B: 1.229 / SU ML: 0.044 / Average fsc free: 0.9824 / Average fsc work: 0.9882 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 1775 5.144 %0.05
Rwork0.143 32732 --
all0.144 ---
obs-34507 88.559 %-
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: 14.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.138 Å20.241 Å20.458 Å2
2---0.139 Å2-0.339 Å2
3---0.298 Å2
Refinement stepCycle: LAST / Resolution: 1.62→36.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 77 141 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122667
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162509
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.6573638
X-RAY DIFFRACTIONr_angle_other_deg0.5781.5725807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.132512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.78552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29510457
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.02910114
X-RAY DIFFRACTIONr_chiral_restr0.0930.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.2260.2529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22397
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21341
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.210
X-RAY DIFFRACTIONr_nbd_other0.1470.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.213
X-RAY DIFFRACTIONr_mcbond_it1.4381.241259
X-RAY DIFFRACTIONr_mcbond_other1.4381.241259
X-RAY DIFFRACTIONr_mcangle_it2.1542.2271572
X-RAY DIFFRACTIONr_mcangle_other2.1532.2281573
X-RAY DIFFRACTIONr_scbond_it3.0591.5631408
X-RAY DIFFRACTIONr_scbond_other3.0591.5631408
X-RAY DIFFRACTIONr_scangle_it4.7042.6972066
X-RAY DIFFRACTIONr_scangle_other4.7032.6972067
X-RAY DIFFRACTIONr_lrange_it5.46714.6563089
X-RAY DIFFRACTIONr_lrange_other5.46114.1263066
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
1.62-1.6620.1831320.14324350.14528730.980.98789.34910.13
1.662-1.7070.1881250.13823810.14127990.9790.98989.5320.128
1.707-1.7570.1881360.13523170.13827600.9810.98988.87680.125
1.757-1.8110.1771310.13522440.13726700.9820.98988.95130.126
1.811-1.870.171190.13621040.13725380.9810.98987.58870.129
1.87-1.9360.1981050.1419900.14324730.9780.98884.71490.132
1.936-2.0080.175930.13917960.14124060.9820.98978.51210.135
2.008-2.090.1591120.14320010.14422830.9830.98892.55370.14
2.09-2.1830.1731030.14119190.14322100.9820.98991.49320.14
2.183-2.2890.176960.14218220.14421020.980.98891.24640.142
2.289-2.4120.176840.13817460.13920240.9840.98990.4150.139
2.412-2.5580.173850.13816420.1419210.9840.98989.90110.14
2.558-2.7330.138860.13314320.13417940.9890.98984.61540.137
2.733-2.9510.168710.14612750.14716590.9840.98781.13320.154
2.951-3.2310.182700.15813760.15915350.9810.98594.2020.168
3.231-3.6080.175650.16112470.16214050.9820.98593.38080.176
3.608-4.160.125490.1410530.13912080.990.98991.22520.157
4.16-5.0790.171510.1318470.13310400.9890.99286.34620.149
5.079-7.1140.17380.1726730.1728030.9850.98788.5430.189
7.114-36.6740.12240.1364320.1354600.9920.98799.13040.162

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