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- PDB-2agt: Aldose Reductase Mutant Leu 300 Pro complexed with Fidarestat -

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Basic information

Entry
Database: PDB / ID: 2agt
TitleAldose Reductase Mutant Leu 300 Pro complexed with Fidarestat
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / NADP / Fidarestat
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / 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. / 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
CITRIC ACID / Chem-FID / 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
AuthorsPetrova, T. / Steuber, H. / Hazemann, I. / Cousido-Siah, A. / Mitschler, A. / Chung, R. / Oka, M. / Klebe, G. / El-Kabbani, O. / Joachimiak, A. / Podjarny, A.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Factorizing Selectivity Determinants of Inhibitor Binding toward Aldose and Aldehyde Reductases: Structural and Thermodynamic Properties of the Aldose Reductase Mutant Leu300Pro-Fidarestat Complex
Authors: Petrova, T. / Steuber, H. / Hazemann, I. / Cousido-Siah, A. / Mitschler, A. / Chung, R. / Oka, M. / Klebe, G. / El-Kabbani, O. / Joachimiak, A. / Podjarny, A.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4155
Polymers36,1651
Non-polymers1,2504
Water10,539585
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.118, 66.724, 47.092
Angle α, β, γ (deg.)90.00, 92.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aldose reductase / / AR / Aldehyde reductase


Mass: 36164.578 Da / Num. of mol.: 1 / Mutation: L300P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15121, aldose reductase

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Non-polymers , 5 types, 589 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-FID / (2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE / FIDARESTAT / Fidarestat


Mass: 279.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10FN3O4 / Comment: inhibitor*YM
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65255 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 24, 2004
Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65255 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 163312 / Num. obs: 163149 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.057 / Net I/σ(I): 18.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.51 / Rsym value: 0.386 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PWM

1pwm


Resolution: 1→50 Å / Num. parameters: 35133 / Num. restraintsaints: 52767 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1289 8161 5 %RANDOM
Rwork0.1055 ---
all0.1059 163149 --
obs0.1059 163062 99.8 %-
Refine analyzeNum. disordered residues: 141 / Occupancy sum hydrogen: 2463.93 / Occupancy sum non hydrogen: 3146.63
Refinement stepCycle: LAST / Resolution: 1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 82 587 3894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0307
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.11

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