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- PDB-1t41: Crystal structure of human aldose reductase complexed with NADP a... -

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Basic information

Entry
Database: PDB / ID: 1t41
TitleCrystal structure of human aldose reductase complexed with NADP and IDD552
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 / 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
Chem-ID5 / 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: 1.05 Å
AuthorsRuiz, F. / Hazemann, I. / Mitschler, A. / Chevrier, B. / Schneider, T. / Joachimiak, A. / Karplus, M. / Podjarny, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48.
Authors: Ruiz, F. / Hazemann, I. / Mitschler, A. / Joachimiak, A. / Schneider, T. / Karplus, M. / Podjarny, A.
History
DepositionApr 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: 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 1.4Mar 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)37,0563
Polymers35,8981
Non-polymers1,1582
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.057, 47.525, 40.028
Angle α, β, γ (deg.)67.32, 76.79, 75.82
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aldose reductase / AR / Aldehyde 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-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-ID5 / [5-FLUORO-2-({[(4,5,7-TRIFLUORO-1,3-BENZOTHIAZOL-2-YL)METHYL]AMINO}CARBONYL)PHENOXY]ACETIC ACID / IDD552


Mass: 414.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10F4N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6000, TrisHCl Buffer, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.90042 / Wavelength: 0.90042 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 2002
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90042 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. all: 168827 / Num. obs: 151945 / % possible obs: 91.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.038 / Net I/σ(I): 20.4
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.85 / Rsym value: 0.358 / % possible all: 73.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALDOSE REDUCTASE HOLOENZYME

Resolution: 1.05→10 Å / Num. parameters: 29053 / Num. restraintsaints: 39024 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1333 3198 5 %RANDOM
Rwork0.1083 ---
all0.1084 134230 --
obs0.1084 151945 93.8 %-
Displacement parametersBiso mean: 13 Å2
Refine analyzeNum. disordered residues: 83 / Occupancy sum hydrogen: 2435.01 / Occupancy sum non hydrogen: 2929.2
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 80 355 3222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.049
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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