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- PDB-1z8a: Human Aldose Reductase complexed with novel Sulfonyl-pyridazinone... -

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Basic information

Entry
Database: PDB / ID: 1z8a
TitleHuman Aldose Reductase complexed with novel Sulfonyl-pyridazinone Inhibitor
Componentsaldose reductase
KeywordsOXIDOREDUCTASE / Protein-Ligand complex / TIM-barrel / double conformation
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
Chem-62P / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å
AuthorsSteuber, H. / Zentgraf, M. / Podjarny, A. / Heine, A. / Klebe, G.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.
Authors: Steuber, H. / Zentgraf, M. / Podjarny, A. / Heine, A. / Klebe, G.
History
DepositionMar 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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)36,9663
Polymers35,8981
Non-polymers1,0682
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.39, 66.86, 47.37
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number4
Space group name H-MP1211

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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: GenBank: 178489, UniProt: P15121*PLUS, 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-62P / 6-[(5-CHLORO-3-METHYL-1-BENZOFURAN-2-YL)SULFONYL]PYRIDAZIN-3(2H)-ONE


Mass: 324.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9ClN2O4S / Details: synthesized
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium citrate, PEG 6000, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91838 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 28, 2004 / Details: Silicon, active surface 50 nm Rh-coated
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 0.95→15 Å / Num. all: 188551 / Num. obs: 188551 / % possible obs: 97.6 % / Redundancy: 2.9 % / Rsym value: 0.045
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 8851 / Rsym value: 0.378 / % possible all: 91.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1el3

1el3


Resolution: 0.95→15 Å / Num. parameters: 27763 / Num. restraintsaints: 34790 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.142 9067 -RANDOM
Rwork0.122 ---
all0.122 181085 --
obs0.122 181085 100 %-
Refine analyzeNum. disordered residues: 28 / Occupancy sum hydrogen: 2520.17 / Occupancy sum non hydrogen: 2950.38
Refinement stepCycle: LAST / Resolution: 0.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 69 375 3081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.103
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.097
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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