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- PDB-3rx3: Crystal Structure of Human Aldose Reductase Complexed with Sulindac -

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Basic information

Entry
Database: PDB / ID: 3rx3
TitleCrystal Structure of Human Aldose Reductase Complexed with Sulindac
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 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-SUZ / 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. / Chen, J. / Luo, H. / Hu, X.
CitationJournal: Febs Lett. / Year: 2012
Title: The molecular basis for inhibition of sulindac and its metabolites towards human aldose reductase.
Authors: Zheng, X. / Zhang, L. / Zhai, J. / Chen, Y. / Luo, H. / Hu, X.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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)39,1703
Polymers38,0701
Non-polymers1,1002
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.153, 66.726, 49.319
Angle α, β, γ (deg.)90.00, 92.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aldose reductase / hAR / 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-SUZ / [(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid / SULINDAC


Mass: 356.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM ammonium citrate, pH5.0, 7.5% 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: Mar 6, 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→24.05 Å / Num. all: 23833 / Num. obs: 23833 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.90004→2 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US0

1us0


Resolution: 1.9→24.05 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1193 5.06 %RANDOM
Rwork0.1504 ---
all0.1529 23556 --
obs0.1529 23556 97.52 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.714 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3654 Å2-0 Å21.3045 Å2
2---0.1555 Å20 Å2
3----1.2099 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 73 414 3018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072714
X-RAY DIFFRACTIONf_angle_d1.133710
X-RAY DIFFRACTIONf_dihedral_angle_d14.6131020
X-RAY DIFFRACTIONf_chiral_restr0.071410
X-RAY DIFFRACTIONf_plane_restr0.005469
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 (%)
1.9-1.97610.21831230.1589212984
1.9761-2.0660.21951220.1486243197
2.066-2.17480.19581360.148251499
2.1748-2.3110.22831310.1529252199
2.311-2.48920.2621360.1633254299
2.4892-2.73940.22361350.16272509100
2.7394-3.13510.19661320.15892552100
3.1351-3.94710.16071390.13862569100
3.9471-24.0520.1791390.14142596100

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