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- PDB-5liu: Crystal structure of human AKR1B10 complexed with NADP+ and the i... -

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Basic information

Entry
Database: PDB / ID: 5liu
TitleCrystal structure of human AKR1B10 complexed with NADP+ and the inhibitor IDD388
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / alpha-beta TIM barrel / cytosol / aldo-keto reductase / halogenated ligand
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / NADP-retinol dehydrogenase / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / retinoid metabolic process / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / 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-388 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Fanfrlik, J. / Kamlar, M. / Vesely, J. / Hobza, P. / Podjarny, A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors.
Authors: Cousido-Siah, A. / Ruiz, F.X. / Fanfrlik, J. / Gimenez-Dejoz, J. / Mitschler, A. / Kamlar, M. / Vesely, J. / Ajani, H. / Pares, X. / Farres, J. / Hobza, P. / Podjarny, A.D.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Aldo-keto reductase family 1 member B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6164
Polymers36,3941
Non-polymers1,2223
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.393, 79.393, 50.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Aldo-keto reductase family 1 member B10 / ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase ...ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase / SI reductase


Mass: 36394.035 Da / Num. of mol.: 1 / Mutation: K125R, V301L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Production host: Escherichia coli (E. coli)
References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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-388 / (2-{[(4-BROMO-2-FLUOROBENZYL)AMINO]CARBONYL}-5-CHLOROPHENOXY)ACETIC ACID / IDD388


Mass: 416.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12BrClFNO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% PEG 6000, 100 mM sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 35928 / % possible obs: 88.1 % / Redundancy: 2.5 % / Rsym value: 0.058 / Net I/σ(I): 15.36
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.78 / % possible all: 61.5

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUA

1zua


Resolution: 1.75→25.987 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1900 5.29 %Random 5%
Rwork0.2079 ---
obs0.2102 35928 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 76 170 2815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072751
X-RAY DIFFRACTIONf_angle_d1.1473738
X-RAY DIFFRACTIONf_dihedral_angle_d14.2021050
X-RAY DIFFRACTIONf_chiral_restr0.076399
X-RAY DIFFRACTIONf_plane_restr0.005466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7457-1.78930.2571680.28272407X-RAY DIFFRACTION93
1.7893-1.83760.27071660.28052400X-RAY DIFFRACTION94
1.8376-1.89160.29371280.27132415X-RAY DIFFRACTION95
1.8916-1.95260.25151380.26012415X-RAY DIFFRACTION95
1.9526-2.02220.26851260.23692444X-RAY DIFFRACTION95
2.0222-2.1030.26451460.24942422X-RAY DIFFRACTION94
2.103-2.19850.25651560.23092409X-RAY DIFFRACTION94
2.1985-2.31410.29421260.24792417X-RAY DIFFRACTION95
2.3141-2.45860.31291340.24752437X-RAY DIFFRACTION95
2.4586-2.64770.30941040.23942456X-RAY DIFFRACTION96
2.6477-2.91280.31521200.22382442X-RAY DIFFRACTION95
2.9128-3.33110.24321300.20762449X-RAY DIFFRACTION95
3.3311-4.1850.23241280.16182409X-RAY DIFFRACTION95
4.185-16.25920.1971300.15342434X-RAY DIFFRACTION95

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