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- PDB-8fh9: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -

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Basic information

Entry
Database: PDB / ID: 8fh9
TitleCrystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-007
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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / epithelial cell maturation / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / 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-XYK / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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-007
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)37,3778
Polymers35,8981
Non-polymers1,4797
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.179, 46.888, 47.296
Angle α, β, γ (deg.)75.478, 67.366, 76.634
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: 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
#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-XYK / (4-oxo-3-{[5-(trifluoromethyl)-1,3-benzothiazol-2-yl]methyl}-3,4-dihydrothieno[3,4-d]pyridazin-1-yl)acetic acid


Mass: 425.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10F3N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
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: 0.97946 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: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→36.688 Å / Num. obs: 30424 / % possible obs: 90.7 % / 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): 14.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.187 / Num. unique obs: 1727 / CC1/2: 0.967 / Rpim(I) all: 0.187 / Rrim(I) all: 0.265

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.688 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.151 / SU B: 1.729 / SU ML: 0.058 / Average fsc free: 0.979 / Average fsc work: 0.9868 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 1516 4.983 %0.05
Rwork0.1501 28905 --
all0.152 ---
obs-30421 90.666 %-
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: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.172 Å2-0.032 Å20.58 Å2
2---0.761 Å2-0.495 Å2
3---0.717 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 96 148 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162535
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.6583647
X-RAY DIFFRACTIONr_angle_other_deg0.6821.5725864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.875.71414
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.97652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22210457
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.91410114
X-RAY DIFFRACTIONr_chiral_restr0.1150.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.220.2548
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22490
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2124
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.215
X-RAY DIFFRACTIONr_nbd_other0.1850.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.29
X-RAY DIFFRACTIONr_mcbond_it1.941.4871259
X-RAY DIFFRACTIONr_mcbond_other1.9391.4881259
X-RAY DIFFRACTIONr_mcangle_it2.6492.6711572
X-RAY DIFFRACTIONr_mcangle_other2.6492.6711573
X-RAY DIFFRACTIONr_scbond_it3.3451.8251422
X-RAY DIFFRACTIONr_scbond_other3.3441.8261423
X-RAY DIFFRACTIONr_scangle_it5.1543.1762075
X-RAY DIFFRACTIONr_scangle_other5.1533.1762076
X-RAY DIFFRACTIONr_lrange_it6.0417.073080
X-RAY DIFFRACTIONr_lrange_other6.01916.6623063
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
1.7-1.7440.211950.16121740.16325200.9740.98290.03970.143
1.744-1.7920.1761150.14720080.14923540.9770.98590.18690.129
1.792-1.8440.2041060.13920290.14223560.9760.98790.61970.123
1.844-1.90.218940.14419600.14723130.9720.98688.80240.125
1.9-1.9620.1811000.14717600.14922050.9780.98584.35370.13
1.962-2.0310.188860.13518660.13821180.9780.98992.16240.124
2.031-2.1070.178900.14218180.14420720.9790.98892.08490.133
2.107-2.1930.183900.13717410.13919900.9790.98992.010.129
2.193-2.290.165960.13315860.13518790.9820.98989.51570.126
2.29-2.4020.153660.13215260.13318420.9820.98986.42780.128
2.402-2.5310.172810.13215420.13417290.9820.9993.86930.128
2.531-2.6840.194750.13414490.13716520.9760.98992.25180.131
2.684-2.8680.162790.13513530.13615510.9820.98992.32750.136
2.868-3.0960.155660.14611800.14714240.9850.98887.50.152
3.096-3.3890.177650.15112010.15313330.9820.98694.97370.162
3.389-3.7850.186610.16710320.16911690.9830.98493.49870.182
3.785-4.3630.161520.1569240.15610620.9860.98691.90210.175
4.363-5.3250.199410.1727930.1748950.9830.98793.18440.203
5.325-7.4520.248390.2256010.2276840.9770.97993.56730.253
7.452-36.6880.188190.1813620.1824030.9750.9794.54090.211

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