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- PDB-1us0: Human Aldose Reductase in complex with NADP+ and the inhibitor ID... -

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Basic information

Entry
Database: PDB / ID: 1us0
TitleHuman Aldose Reductase in complex with NADP+ and the inhibitor IDD594 at 0.66 Angstrom
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE / NADP / IDD594
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
CITRIC ACID / IDD594 / Chem-NDP / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.66 Å
AuthorsHoward, E.I. / Sanishvili, R. / Cachau, R.E. / Mitschler, A. / Chevrier, B. / Barth, P. / Lamour, V. / Van Zandt, M. / Sibley, E. / Bon, C. ...Howard, E.I. / Sanishvili, R. / Cachau, R.E. / Mitschler, A. / Chevrier, B. / Barth, P. / Lamour, V. / Van Zandt, M. / Sibley, E. / Bon, C. / Moras, D. / Schneider, T.R. / Joachimiak, A. / Podjarny, A.
CitationJournal: Proteins / Year: 2004
Title: Ultrahigh Resolution Drug Design I: Details of Interactions in Human Aldose Reductase-Inhibitor Complex at 0.66 A.
Authors: Howard, E.I. / Sanishvili, R. / Cachau, R.E. / Mitschler, A. / Chevrier, B. / Barth, P. / Lamour, V. / Van Zandt, M. / Sibley, E. / Bon, C. / Moras, D. / Schneider, T.R. / Joachimiak, A. / Podjarny, A.
History
DepositionNov 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method

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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)37,4445
Polymers35,8981
Non-polymers1,5464
Water11,043613
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.280, 66.590, 47.260
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALDOSE REDUCTASE / / ALDEHYDE REDUCTASE


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15121, aldose reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-LDT / IDD594 / [2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)-5-FLUORO-PHENOXY]-ACETIC ACID


Mass: 416.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12BrF2NO3S
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE NADPH-DEPENDENT REDUCTION OF A WIDE RANGE OF CARBONYL-CONTAINING COMPOUNDS INTO ...CATALYZES THE NADPH-DEPENDENT REDUCTION OF A WIDE RANGE OF CARBONYL-CONTAINING COMPOUNDS INTO CORRESPONDING ALCOHOLS. THE PROTEIN IS THOUGHT TO PLAY A KEY ROLE IN DIABETIC COMPLICATIONS OF THREE OTHER TARGET TISSUES, NAMELY, NERVE, KIDNEY AND RETINA.
Sequence detailsTHE CONFLICT ANNOTATED IN THE SEQADV CARDS BELOW HAS HAS BEEN DESCRIBED IN J.BIOL.CHEM. 264:14775 ...THE CONFLICT ANNOTATED IN THE SEQADV CARDS BELOW HAS HAS BEEN DESCRIBED IN J.BIOL.CHEM. 264:14775 (1989). THE MEDLINE ID FOR THIS REFERENCE IS 89359274 AND THE PUBMED ID FOR THE SAME IS 2504709.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growpH: 5
Details: AS DESCRIBED IN LAMOUR ET AL. (1999) ACTA CRYSTALL. SECTION D 55:721-723, pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.653
DetectorType: ANL / Detector: CCD / Date: Apr 19, 1999
Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITTAL HORIZONTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.653 Å / Relative weight: 1
ReflectionResolution: 0.66→20 Å / Num. obs: 511265 / % possible obs: 89.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 14.5
Reflection shellResolution: 0.66→0.68 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.4 / % possible all: 75.4

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXLphasing
RefinementMethod to determine structure: MAD / Resolution: 0.66→20 Å / Num. parameters: 33158 / Num. restraintsaints: 46316 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1032 25587 5 %RANDOM
all0.0938 511265 --
obs0.0936 -0.4 %-
Solvent computationSolvent model: KRETSINGER
Refine analyzeNum. disordered residues: 199 / Occupancy sum hydrogen: 2445.24 / Occupancy sum non hydrogen: 3054.25
Refinement stepCycle: LAST / Resolution: 0.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 98 613 3203
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_planes0.331
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.118
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.083

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