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- PDB-4qxi: Crystal structure of human AR complexed with NADP+ and AK198 -

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Basic information

Entry
Database: PDB / ID: 4qxi
TitleCrystal structure of human AR complexed with NADP+ and AK198
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-I98 / 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: 0.867 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Fanfrlik, J. / Hobza, P. / Podjarny, A.D.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition.
Authors: Fanfrlik, J. / Ruiz, F.X. / Kadlcikova, A. / Rezac, J. / Cousido-Siah, A. / Mitschler, A. / Haldar, S. / Lepsik, M. / Kolar, M.H. / Majer, P. / Podjarny, A.D. / Hobza, P.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations / Category: citation / database_2 / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,9943
Polymers35,8981
Non-polymers1,0962
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.403, 66.542, 47.311
Angle α, β, γ (deg.)90.00, 92.34, 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 BL21(DE3) (bacteria) / 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-I98 / {2-[(4-amino-2-fluorobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid


Mass: 352.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14ClFN2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS BASED ON GENBANK DATABASE AAA51714.

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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: 43.17 %
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: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 3, 2014
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.867→50 Å / Num. all: 219664 / Num. obs: 219664 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 6.31 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
0.87-0.930.356172.5
0.9-0.943.10.242175.3
0.94-0.983.50.163184.7
0.98-1.033.80.109191.2
1.03-1.14.10.076190.2
1.1-1.184.50.059188.8
1.18-1.34.90.053194.8
1.3-1.495.50.047191.4
1.49-1.877.10.041196
1.87-505.90.032189.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: dev_1624)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1US0

1us0


Resolution: 0.867→27.589 Å / SU ML: 0.06 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 12.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1448 10612 4.86 %Random
Rwork0.1336 ---
all0.1341 219631 --
obs0.1341 219631 87.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.867→27.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 72 493 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062781
X-RAY DIFFRACTIONf_angle_d1.3173808
X-RAY DIFFRACTIONf_dihedral_angle_d11.8621066
X-RAY DIFFRACTIONf_chiral_restr0.052423
X-RAY DIFFRACTIONf_plane_restr0.008483
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.8672-0.8770.25615040.22661022464
0.877-0.88730.21775830.19881150073
0.8873-0.89820.1976880.18071179075
0.8982-0.90950.1786150.16471214777
0.9095-0.92150.15186380.15031216378
0.9215-0.93410.15035320.1431150272
0.9341-0.94750.15346580.13651213377
0.9475-0.96160.14586820.12781384587
0.9616-0.97660.13967660.12661397589
0.9766-0.99270.13216800.12061441991
0.9927-1.00980.12836520.11441462491
1.0098-1.02810.12367230.11521457092
1.0281-1.04790.12337190.11061446892
1.0479-1.06930.11817650.10691438491
1.0693-1.09260.11197290.10381396488
1.0926-1.1180.10316430.10571247479
1.118-1.14590.11297370.10371477193
1.1459-1.17690.11868060.10691489795
1.1769-1.21150.11376860.10931508395
1.2115-1.25070.12567650.11481499495
1.2507-1.29540.12447800.11881513995
1.2954-1.34720.13467740.12171499595
1.3472-1.40850.13797390.1251489394
1.4085-1.48280.13575960.12851374786
1.4828-1.57570.13268670.12571463294
1.5757-1.69730.1347600.12991549197
1.6973-1.86810.14957210.13941538797
1.8681-2.13830.1619220.14571510996
2.1383-2.69370.17717630.15291362387
2.6937-27.60310.16016730.15371375087

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