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- PDB-4lb3: Crystal structure of human AR complexed with NADP+ and {5-chloro-... -

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Basic information

Entry
Database: PDB / ID: 4lb3
TitleCrystal structure of human AR complexed with NADP+ and {5-chloro-2-[(2-fluoro-4-iodobenzyl)carbamoyl]phenoxy}acetic acid
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / TIM barrel / Aldose reductase / diabetes / Halogenated compound / Cytosolic
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
Chem-M15 / 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: 0.8 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Fanfrlik, J. / Kolar, M. / Hobza, P. / Podjarny, A.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Modulation of aldose reductase inhibition by halogen bond tuning.
Authors: Fanfrlik, J. / Kolar, M. / Kamlar, M. / Hurny, D. / Ruiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Rezac, J. / Munusamy, E. / Lepsik, M. / Matejicek, P. / Vesely, J. / Podjarny, A. / Hobza, P.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 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_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

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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)37,1053
Polymers35,8981
Non-polymers1,2072
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.244, 66.845, 47.244
Angle α, β, γ (deg.)90.00, 92.46, 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: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15b / 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-M15 / {5-chloro-2-[(2-fluoro-4-iodobenzyl)carbamoyl]phenoxy}acetic acid


Mass: 463.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12ClFINO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO UNIPROT SEQUENCE DATABASE, THERE IS A L->I SEQUENCE CONFLICT AT THIS POSITION.

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM ammonium citrate, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.70849 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. all: 314390 / Num. obs: 314390 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
0.8-0.832.70.316189.8
0.83-0.863.80.25197.1
0.86-0.94.30.181197.1
0.9-0.954.80.131198.5
0.95-1.015.20.096197.9
1.01-1.096.40.0721100
1.09-1.26.30.055199.9
1.2-1.376.70.0481100
1.37-1.726.50.04199.9
1.72-506.40.03199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1US0

1us0


Resolution: 0.8→33.353 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.05 / σ(F): 1.34 / Phase error: 9.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1308 15893 5.06 %
Rwork0.1305 --
obs0.1306 314348 97.86 %
all-314348 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.1789 Å2
Refinement stepCycle: LAST / Resolution: 0.8→33.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 72 592 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072713
X-RAY DIFFRACTIONf_angle_d1.3863708
X-RAY DIFFRACTIONf_dihedral_angle_d13.1061033
X-RAY DIFFRACTIONf_chiral_restr0.085409
X-RAY DIFFRACTIONf_plane_restr0.008471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8-0.80860.21783880.23027669X-RAY DIFFRACTION75
0.8086-0.81810.1945020.19839435X-RAY DIFFRACTION94
0.8181-0.82810.18035300.17999771X-RAY DIFFRACTION96
0.8281-0.83860.15515240.16159827X-RAY DIFFRACTION97
0.8386-0.84960.14995220.14949859X-RAY DIFFRACTION97
0.8496-0.86130.14195110.149847X-RAY DIFFRACTION97
0.8613-0.87360.12915080.13659665X-RAY DIFFRACTION95
0.8736-0.88660.13665350.13179787X-RAY DIFFRACTION97
0.8866-0.90050.13035520.129310047X-RAY DIFFRACTION99
0.9005-0.91520.11045320.111110025X-RAY DIFFRACTION99
0.9152-0.9310.11015350.10710004X-RAY DIFFRACTION99
0.931-0.94790.11314990.10649954X-RAY DIFFRACTION98
0.9479-0.96620.10395280.105310011X-RAY DIFFRACTION98
0.9662-0.98590.09935430.10369740X-RAY DIFFRACTION96
0.9859-1.00730.09965470.100210061X-RAY DIFFRACTION99
1.0073-1.03080.10225270.098610141X-RAY DIFFRACTION100
1.0308-1.05650.09965470.097710118X-RAY DIFFRACTION100
1.0565-1.08510.09174990.095410196X-RAY DIFFRACTION100
1.0851-1.1170.0985270.09610191X-RAY DIFFRACTION100
1.117-1.15310.10185470.097110206X-RAY DIFFRACTION100
1.1531-1.19430.10426120.09910052X-RAY DIFFRACTION100
1.1943-1.24210.11335510.105810148X-RAY DIFFRACTION100
1.2421-1.29870.10955360.110710177X-RAY DIFFRACTION100
1.2987-1.36710.12115570.114210157X-RAY DIFFRACTION100
1.3671-1.45280.12415310.122810204X-RAY DIFFRACTION100
1.4528-1.5650.11955490.124610145X-RAY DIFFRACTION100
1.565-1.72250.14384950.134710231X-RAY DIFFRACTION100
1.7225-1.97170.14945580.148710223X-RAY DIFFRACTION100
1.9717-2.4840.15545410.155810244X-RAY DIFFRACTION100
2.484-33.3820.15275600.158210320X-RAY DIFFRACTION100

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