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- PDB-8fh7: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -

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Basic information

Entry
Database: PDB / ID: 8fh7
TitleCrystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-003
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor Complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR 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 / Chem-XY0 / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
Authors: Arenas, R. / Wilson, D.K.
History
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,2326
Polymers35,9141
Non-polymers1,3175
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.186, 46.957, 47.379
Angle α, β, γ (deg.)75.771, 67.466, 76.871
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: 35914.340 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-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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 44.22 %
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: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→36.733 Å / Num. obs: 44438 / % possible obs: 81.7 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 11.3
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2 % / Rmerge(I) obs: 0.418 / Num. unique obs: 2146 / CC1/2: 0.687 / Rpim(I) all: 0.418 / Rrim(I) all: 0.591

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→36.733 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.147 / SU B: 1.032 / SU ML: 0.039 / Average fsc free: 0.9769 / Average fsc work: 0.9837 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 2219 4.994 %0.05
Rwork0.1451 42217 --
all0.146 ---
obs-44436 81.691 %-
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: 16.608 Å2
Baniso -1Baniso -2Baniso -3
1--0.106 Å20.099 Å20.53 Å2
2---0.158 Å2-0.313 Å2
3---0.481 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 86 180 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162521
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6563633
X-RAY DIFFRACTIONr_angle_other_deg0.5841.5725830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.367512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.03352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66210454
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.80810114
X-RAY DIFFRACTIONr_chiral_restr0.0930.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.220.2540
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22448
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21332
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2124
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.211
X-RAY DIFFRACTIONr_nbd_other0.1880.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.28
X-RAY DIFFRACTIONr_mcbond_it1.7711.5031259
X-RAY DIFFRACTIONr_mcbond_other1.7711.5031259
X-RAY DIFFRACTIONr_mcangle_it2.6512.6991572
X-RAY DIFFRACTIONr_mcangle_other2.652.71573
X-RAY DIFFRACTIONr_scbond_it3.271.8541411
X-RAY DIFFRACTIONr_scbond_other3.2691.8551412
X-RAY DIFFRACTIONr_scangle_it5.0293.2222061
X-RAY DIFFRACTIONr_scangle_other5.0283.2222062
X-RAY DIFFRACTIONr_lrange_it5.90517.4793074
X-RAY DIFFRACTIONr_lrange_other5.8817.343052
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
1.45-1.4880.2751670.25131100.25240740.9560.96180.43690.242
1.488-1.5280.2491670.21429730.21638630.9620.9781.2840.2
1.528-1.5730.2391680.19128300.19338240.9650.97678.39960.175
1.573-1.6210.1921620.1727850.17137110.9740.98179.41260.154
1.621-1.6740.1971480.15629590.15835790.9770.98486.8120.141
1.674-1.7330.1661520.14628810.14734650.9830.98787.53250.132
1.733-1.7980.2041500.14127180.14433310.9760.98886.10030.128
1.798-1.8710.1661350.14125900.14232390.9830.98884.13090.128
1.871-1.9540.1961030.14323650.14530880.9780.98879.92230.132
1.954-2.0490.1571310.13721700.13829540.9860.98977.89440.13
2.049-2.1590.1531090.13322440.13327980.9850.99184.09580.129
2.159-2.290.1631090.13620790.13726420.9830.9982.8160.136
2.29-2.4470.156840.13119260.13325320.9820.9979.38390.134
2.447-2.6430.158930.13217470.13423180.9840.98979.37880.137
2.643-2.8930.152720.1314430.13121330.9880.9971.02670.139
2.893-3.2320.184770.1415220.14219320.9810.98882.7640.156
3.232-3.7270.175640.14213380.14317050.9830.98882.22870.162
3.727-4.5540.098520.12511330.12314480.9940.99181.8370.149
4.554-6.3910.16470.1638330.16311200.990.9978.57140.195
6.391-36.7330.172290.1545710.1556370.970.98494.19150.187

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