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- PDB-4lau: Crystal structure of human AR complexed with NADP+ and {2-[(4-bro... -

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Basic information

Entry
Database: PDB / ID: 4lau
TitleCrystal structure of human AR complexed with NADP+ and {2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / TIM barrel / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-W8X / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.843 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)37,0403
Polymers35,8981
Non-polymers1,1422
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.328, 67.047, 47.347
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 / 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-W8X / {2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid


Mass: 398.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13BrClNO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
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: Nov 30, 2011
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 0.84→50 Å / Num. obs: 269672 / % possible obs: 83.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
0.84-0.871.80.286169.2
0.87-0.91.80.207181.7
0.9-0.951.70.14181.2
0.95-11.90.098184.4
1-1.061.80.065184.3
1.06-1.141.80.045185
1.14-1.251.80.034187.8
1.25-1.441.80.029188.5
1.44-1.811.80.022191.7
1.81-501.60.017185.2

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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: 0.843→15.869 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.05 / σ(F): 1.35 / Phase error: 11.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1421 13648 5.06 %
Rwork0.1379 --
obs0.1381 269672 97.7 %
all-269671 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.2018 Å2
Refinement stepCycle: LAST / Resolution: 0.843→15.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 71 590 3186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072712
X-RAY DIFFRACTIONf_angle_d1.3693706
X-RAY DIFFRACTIONf_dihedral_angle_d12.6271033
X-RAY DIFFRACTIONf_chiral_restr0.088409
X-RAY DIFFRACTIONf_plane_restr0.008471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.843-0.85270.1954440.1937805X-RAY DIFFRACTION90
0.8527-0.86270.17344420.17558628X-RAY DIFFRACTION98
0.8627-0.87320.16374460.16358571X-RAY DIFFRACTION99
0.8732-0.88430.17274500.15928569X-RAY DIFFRACTION98
0.8843-0.89590.1614650.15478583X-RAY DIFFRACTION98
0.8959-0.90820.15654230.14778523X-RAY DIFFRACTION98
0.9082-0.92110.14064230.13778578X-RAY DIFFRACTION98
0.9211-0.93490.14114650.1318551X-RAY DIFFRACTION98
0.9349-0.94950.13974790.12598536X-RAY DIFFRACTION98
0.9495-0.96510.12814840.12218568X-RAY DIFFRACTION99
0.9651-0.98170.12534620.12128565X-RAY DIFFRACTION99
0.9817-0.99950.11844480.11728643X-RAY DIFFRACTION98
0.9995-1.01880.12574480.12068551X-RAY DIFFRACTION98
1.0188-1.03960.1254580.11628548X-RAY DIFFRACTION98
1.0396-1.06220.12174580.10978547X-RAY DIFFRACTION98
1.0622-1.08690.11824770.1098458X-RAY DIFFRACTION98
1.0869-1.1140.10964480.10378676X-RAY DIFFRACTION99
1.114-1.14410.11434640.10468616X-RAY DIFFRACTION99
1.1441-1.17780.10994810.10718607X-RAY DIFFRACTION99
1.1778-1.21580.10954650.10968586X-RAY DIFFRACTION99
1.2158-1.25920.12064700.11748638X-RAY DIFFRACTION99
1.2592-1.30960.12544560.12048615X-RAY DIFFRACTION99
1.3096-1.36920.12984310.12288569X-RAY DIFFRACTION98
1.3692-1.44140.1414450.13058673X-RAY DIFFRACTION99
1.4414-1.53160.12684790.12828657X-RAY DIFFRACTION99
1.5316-1.64970.1394620.13198608X-RAY DIFFRACTION99
1.6497-1.81550.14664550.14468610X-RAY DIFFRACTION98
1.8155-2.07780.16634510.15548533X-RAY DIFFRACTION97
2.0778-2.61590.1634650.16018664X-RAY DIFFRACTION98
2.6159-15.87190.16424040.16747748X-RAY DIFFRACTION87

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