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- PDB-3t42: Human aldose reductase in complex with a nitrile-containing IDD i... -

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Basic information

Entry
Database: PDB / ID: 3t42
TitleHuman aldose reductase in complex with a nitrile-containing IDD inhibitor
ComponentsAldose reductase
Keywordsoxidoreductase/oxidoreductase inhibitor / Tim Barrel / oxidoreductase-oxidoreductase inhibitor complex
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-3T4 / CITRIC ACID / 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: 1.28 Å
AuthorsXu, L. / Cohen, A.E. / Boxer, S.G.
CitationJournal: Biochemistry / Year: 2011
Title: Electrostatic Fields near the Active Site of Human Aldose Reductase: 2. New Inhibitors and Complications Caused by Hydrogen Bonds.
Authors: Xu, L. / Cohen, A.E. / Boxer, S.G.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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)37,5064
Polymers36,1811
Non-polymers1,3253
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.858, 46.963, 46.907
Angle α, β, γ (deg.)76.35, 77.21, 67.79
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36180.621 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
#2: 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
#3: Chemical ChemComp-3T4 / {5-chloro-2-[(4-cyano-3-nitrobenzyl)carbamoyl]phenoxy}acetic acid


Mass: 389.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12ClN3O6
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 298 K / pH: 4.2
Details: The hanging drop method was used to obtain crystals (EasyXtal Tool 24 culture plates, Qiagen). WT hALR2 was co-crystallized with the oxidized form of coenzyme NADP+ (Sigma) and inhibitor 2 ...Details: The hanging drop method was used to obtain crystals (EasyXtal Tool 24 culture plates, Qiagen). WT hALR2 was co-crystallized with the oxidized form of coenzyme NADP+ (Sigma) and inhibitor 2 at room temperature (ratios of protein / inhibitor / coenzyme = 1/2/2). Hanging drops were made by the mixing mother liquor (0.06 M citric acid, 0.04 M Bis-tris propane, 12% (w/v) PEG 3350, pH 4.2) with holoenzyme solution (10 mg/mL, 20 mM hepes, pH 7.0). Crystals were observed after three days of equilibration, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 73538 / % possible obs: 94.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.14 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.4
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.301 / % possible all: 87.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PZN

2pzn


Resolution: 1.28→22.29 Å / SU ML: 0.16 / σ(F): 0.13 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 1860 2.69 %
Rwork0.151 --
obs0.152 69094 88.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.38 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7789 Å21.5685 Å20.4889 Å2
2--3.1947 Å2-0.7156 Å2
3----2.4157 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 88 431 3044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082772
X-RAY DIFFRACTIONf_angle_d1.3413802
X-RAY DIFFRACTIONf_dihedral_angle_d19.4011056
X-RAY DIFFRACTIONf_chiral_restr0.077422
X-RAY DIFFRACTIONf_plane_restr0.006483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2793-1.31390.30941060.27323965X-RAY DIFFRACTION68
1.3139-1.35260.20051260.17344904X-RAY DIFFRACTION84
1.3526-1.39620.29271210.23354455X-RAY DIFFRACTION76
1.3962-1.44610.22211440.17045039X-RAY DIFFRACTION86
1.4461-1.5040.19571340.16874906X-RAY DIFFRACTION84
1.504-1.57240.21831440.17474948X-RAY DIFFRACTION85
1.5724-1.65530.16311520.10725479X-RAY DIFFRACTION94
1.6553-1.7590.17141510.11325469X-RAY DIFFRACTION94
1.759-1.89470.17311560.12325570X-RAY DIFFRACTION95
1.8947-2.08530.19321520.15995479X-RAY DIFFRACTION94
2.0853-2.38670.17021560.14815614X-RAY DIFFRACTION96
2.3867-3.00580.18281600.14175742X-RAY DIFFRACTION98
3.0058-22.28840.13451580.13575664X-RAY DIFFRACTION97

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