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- PDB-2pfh: Complex of Aldose Reductase with NADP+ and simaltaneously bound c... -

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Basic information

Entry
Database: PDB / ID: 2pfh
TitleComplex of Aldose Reductase with NADP+ and simaltaneously bound competetive inhibitors Fidarestat and IDD594. Concentration of Fidarestat in soaking solution is less than concentration of IDD594.
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / NADP / IDD594 / FIDARESTAT
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 / metanephric collecting duct development / all-trans-retinol dehydrogenase (NADP+) activity / 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. / 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 / IDD594 / Chem-NDP / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsPetrova, T. / Hazemann, I. / Cousido, A. / Mitschler, A. / Ginell, S. / Joachimiak, A. / Podjarny, A.
CitationJournal: Proteins / Year: 2012
Title: Crystal packing modifies ligand binding affinity: The case of aldose reductase.
Authors: Cousido-Siah, A. / Petrova, T. / Hazemann, I. / Mitschler, A. / Ruiz, F.X. / Howard, E. / Ginell, S. / Atmanene, C. / Van Dorsselaer, A. / Sanglier-Cianferani, S. / Joachimiak, A. / Podjarny, A.
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Database references
Revision 1.4Oct 17, 2012Group: Database references
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence THERE IS A LEU -> ILE SEQUENCE CONFLICT AT RESIDUE 5 IN THE UNIPORT DATABASE.

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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)37,7597
Polymers35,8981
Non-polymers1,8616
Water11,818656
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.147, 66.553, 47.238
Angle α, β, γ (deg.)90.00, 92.31, 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: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase

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Non-polymers , 6 types, 662 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-LDT / IDD594 / [2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)-5-FLUORO-PHENOXY]-ACETIC ACID


Mass: 416.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12BrF2NO3S
#5: Chemical ChemComp-FID / (2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE / FIDARESTAT


Mass: 279.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10FN3O4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: micro-seeding, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65255
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006
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: 0.85→50 Å / Num. all: 253545 / Num. obs: 240860 / % possible obs: 95.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.32
Reflection shellResolution: 0.85→0.88 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.5 / % possible all: 69.47

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US0

1us0


Resolution: 0.85→50 Å / Num. parameters: 35222 / Num. restraintsaints: 51858 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.0948 12685 5 %RANDOM
Rwork0.0822 ---
obs0.0822 240860 95.4 %-
all-253545 --
Refine analyzeNum. disordered residues: 406 / Occupancy sum hydrogen: 2441.21 / Occupancy sum non hydrogen: 3009.81
Refinement stepCycle: LAST / Resolution: 0.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 119 656 3267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.055
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.121
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.113
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.15
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.082

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