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

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Basic information

Entry
Database: PDB / ID: 4lbr
TitleCrystal structure of human AR complexed with NADP+ and {5-chloro-2-[(2,6-difluoro-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 / 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-4O9 / 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 21, 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)37,1233
Polymers35,8981
Non-polymers1,2252
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)49.223, 66.730, 47.288
Angle α, β, γ (deg.)90.000, 92.590, 90.000
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-4O9 / {5-chloro-2-[(2,6-difluoro-4-iodobenzyl)carbamoyl]phenoxy}acetic acid


Mass: 481.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11ClF2INO4
#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: 43.09 %
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. obs: 297856 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.048 / Χ2: 1.056 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
0.8-0.833.10.346249891.024178.4
0.83-0.8640.283283911.074189
0.86-0.94.50.212291021.078191.3
0.9-0.954.90.156299321.07193.9
0.95-1.015.50.116294381.076192.3
1.01-1.096.70.091305761.058195.8
1.09-1.26.50.071308311.032196.5
1.2-1.376.80.058311581.056197.4
1.37-1.726.60.048315021.064198.4
1.72-506.40.036319371.034198.8

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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→38.556 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9484 / SU ML: 0.05 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 10.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1344 15041 5.05 %Random 5%
Rwork0.1314 ---
obs0.1316 297811 93.11 %-
all-297811 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.95 Å2 / Biso mean: 12.1749 Å2 / Biso min: 2.31 Å2
Refinement stepCycle: LAST / Resolution: 0.8→38.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 73 592 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072714
X-RAY DIFFRACTIONf_angle_d1.3973710
X-RAY DIFFRACTIONf_chiral_restr0.085409
X-RAY DIFFRACTIONf_plane_restr0.008471
X-RAY DIFFRACTIONf_dihedral_angle_d12.3921034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.8-0.80940.2353690.23296898726768
0.8094-0.81890.19624230.2028174859781
0.8189-0.82890.18384380.18278489892784
0.8289-0.83940.15514950.1698691918687
0.8394-0.85050.1724570.169038949589
0.8505-0.86210.14724950.15219252974791
0.8621-0.87440.1554880.15058981946989
0.8744-0.88750.13524600.14059190965091
0.8875-0.90140.13934800.13639490997093
0.9014-0.91610.12965350.11779425996094
0.9161-0.93190.12015100.11495201003094
0.9319-0.94890.10615270.11179442996994
0.9489-0.96710.11285180.110295001001894
0.9671-0.98690.11184550.10869012946789
0.9869-1.00830.1084740.104695341000894
1.0083-1.03180.1115140.101296001011496
1.0318-1.05760.10045360.099496851022196
1.0576-1.08620.1045000.099297241022496
1.0862-1.11820.10355290.097697381026796
1.1182-1.15430.10615030.099798081031197
1.1543-1.19550.10165120.101397831029597
1.1955-1.24340.11215350.107598201035597
1.2434-1.30.10995250.112498451037097
1.3-1.36850.12135450.116398951044098
1.3685-1.45430.12114870.122699881047598
1.4543-1.56650.12155170.122599671048498
1.5665-1.72420.1315480.1337100101055899
1.7242-1.97370.15795590.1468100791063899
1.9737-2.48660.15825570.1563100851064299
2.4866-38.60090.16065500.1563101071065798

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