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- PDB-1pwl: Crystal structure of human Aldose Reductase complexed with NADP a... -

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Basic information

Entry
Database: PDB / ID: 1pwl
TitleCrystal structure of human Aldose Reductase complexed with NADP and Minalrestat
Componentsaldose reductase
KeywordsOXIDOREDUCTASE / ALDOSE REDUCTASE / ATOMIC RESOLUTION / TERNARY COMPLEX / INHIBITOR BINDING
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
Chem-BFI / 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: 1.1 Å
AuthorsEl-Kabbani, O. / Darmanin, C. / Schneider, T.R. / Hazemann, I. / Ruiz, F. / Oka, M. / Joachimiak, A. / Schulze-Briese, C. / Tomizaki, T. / Mitschler, A. / Podjarny, A.
CitationJournal: PROTEINS / Year: 2004
Title: Ultrahigh resolution drug design. II. Atomic resolution structures of human aldose reductase holoenzyme complexed with Fidarestat and Minalrestat: implications for the binding of cyclic imide inhibitors
Authors: El-Kabbani, O. / Darmanin, C. / Schneider, T.R. / Hazemann, I. / Ruiz, F. / Oka, M. / Joachimiak, A. / Schulze-Briese, C. / Tomizaki, T. / Mitschler, A. / Podjarny, A.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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)37,0913
Polymers35,8981
Non-polymers1,1932
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.019, 47.128, 47.367
Angle α, β, γ (deg.)75.71, 67.48, 76.75
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) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-BFI / 2[4-BROMO-2-FLUOROPHENYL)METHYL]-6-FLUOROSPIRO[ISOQUINOLINE-4-(1H),3'-PYRROLIDINE]-1,2',3,5'(2H)-TETRONE / MINALRESTAT


Mass: 449.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H11BrF2N2O4
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 1.64 Å3/Da / Density % sol: 24.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 6000, ammonium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG60001drop
250 mMammonium citrate1droppH5.
320 %PEG60001reservoir
4120 mMammonium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9 / Wavelength: 0.9 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 30, 2001
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.91
ReflectionResolution: 1.1→50 Å / Num. all: 115145 / Num. obs: 115145 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.63 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.6
Reflection shellResolution: 1.1→1.61 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.0921 / Mean I/σ(I) obs: 11.75 / % possible all: 81.5
Reflection
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 81.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALDOSE REDUCTASE HOLOENZYME

Resolution: 1.1→10 Å / Num. parameters: 28902 / Num. restraintsaints: 36371 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1248 6391 5 %RANDOM
Rwork0.0988 ---
all0.0996 115144 --
obs0.0996 115144 92.7 %-
Displacement parametersBiso mean: 13.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.035 Å / Num. disordered residues: 95 / Occupancy sum hydrogen: 2390.21 / Occupancy sum non hydrogen: 2967.93
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 76 429 3208
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_planes0.0276
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.043
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.095
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.124 / Rfactor Rwork: 0.099
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.75
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg8.55
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.095

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