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- PDB-3v35: Aldose reductase complexed with a nitro compound -

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Basic information

Entry
Database: PDB / ID: 3v35
TitleAldose reductase complexed with a nitro compound
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / aldose reductase
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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / epithelial cell maturation / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / 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
DIMETHYLFORMAMIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NTI / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZheng, X. / Zhang, L. / Chen, Y. / Luo, H. / Hu, X.
CitationJournal: Chemmedchem / Year: 2012
Title: Partial inhibition of aldose reductase by nitazoxanide and its molecular basis.
Authors: Zheng, X. / Zhang, L. / Chen, W. / Chen, Y. / Xie, W. / Hu, X.
History
DepositionDec 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Nov 8, 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_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

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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)40,80226
Polymers38,0701
Non-polymers2,73225
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.927, 68.158, 48.934
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / AR / Aldehyde reductase / Aldo-keto reductase family 1 member B1


Mass: 38069.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-NTI / 2-[(5-nitro-1,3-thiazol-2-yl)carbamoyl]phenyl acetate


Mass: 307.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9N3O5S / Comment: medication, antiparasitic, antivirus*YM
#4: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 120mM ammonium citrate pH 5.0, 20% (m/V) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jun 3, 2011
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→24.402 Å / Num. all: 24241 / Num. obs: 24241 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.9-23.30.3563.43437197.3
6.01-24.46.50.03535.6789198.7

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1US0

1us0


Resolution: 1.9→24.402 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 16.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 1232 5.09 %RANDOM
Rwork0.1434 ---
all0.1454 24221 --
obs0.1454 24221 99.55 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.941 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5115 Å2-0 Å2-0.0667 Å2
2--1.949 Å20 Å2
3----2.4606 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 184 269 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072764
X-RAY DIFFRACTIONf_angle_d1.1723740
X-RAY DIFFRACTIONf_dihedral_angle_d18.2481027
X-RAY DIFFRACTIONf_chiral_restr0.077406
X-RAY DIFFRACTIONf_plane_restr0.006484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.97610.22571410.1992244096
1.9761-2.0660.23071380.15432555100
2.066-2.17480.19871340.13962549100
2.1748-2.3110.1781370.13832547100
2.311-2.48930.1841270.13322560100
2.4893-2.73950.20261470.14352568100
2.7395-3.13520.18071270.14512576100
3.1352-3.94730.17121510.12972565100
3.9473-24.40430.14631300.14322629100

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