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- PDB-1iei: CRYSTAL STRUCTURE OF HUMAN ALDOSE REDUCTASE COMPLEXED WITH THE IN... -

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Basic information

Entry
Database: PDB / ID: 1iei
TitleCRYSTAL STRUCTURE OF HUMAN ALDOSE REDUCTASE COMPLEXED WITH THE INHIBITOR ZENARESTAT.
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE / Protein-inhibitor complex / NADP
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. / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-ZES / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKinoshita, T. / Miyake, H. / Fujii, T. / Takakura, S. / Goto, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The structure of human recombinant aldose reductase complexed with the potent inhibitor zenarestat.
Authors: Kinoshita, T. / Miyake, H. / Fujii, T. / Takakura, S. / Goto, T.
History
DepositionApr 9, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALDOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0833
Polymers35,8981
Non-polymers1,1852
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.40, 47.97, 47.66
Angle α, β, γ (deg.)76.2, 76.7, 67.5
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALDOSE REDUCTASE


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, 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
#3: Chemical ChemComp-ZES / [3-(4-BROMO-2-FLUORO-BENZYL)-7-CHLORO-2,4-DIOXO-3,4-DIHYDRO-2H-QUINAZOLIN-1-YL]-ACETIC ACID / ZENARESTAT


Mass: 441.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11BrClFN2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
250 mMcitrate1droppH5.0
37 mM2-mercaptoethanol1drop
41 mMzenarestat1drop
520-22.5 %(w/v)PEG60001reservoir
650 mMcitrate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER
RadiationMonochromator: sillicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 10355 / Num. obs: 9831 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.091 / % possible all: 83.7
Reflection
*PLUS
Num. obs: 10355 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 16.7

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR98.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / σ(F): 2 / σ(I): 1
RfactorNum. reflectionSelection details
Rfree0.199 491 Random
Rwork0.178 --
all-9831 -
obs-9340 -
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 74 186 2773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.039
X-RAY DIFFRACTIONx_angle_d4.4
X-RAY DIFFRACTIONx_dihedral_angle_d29.8
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.178 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg4.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.197 / Rfactor obs: 0.197

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