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- PDB-4gab: Human AKR1B10 mutant V301L complexed with NADP+ and fidarestat -

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Basic information

Entry
Database: PDB / ID: 4gab
TitleHuman AKR1B10 mutant V301L complexed with NADP+ and fidarestat
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / tim barrel / aldo-keto reductase
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / 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. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / 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. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / 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-FID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5971 Å
AuthorsCousido-Siah, A. / Ruiz Figueras, F.X. / Mitschler, A. / Podjarny, A.
CitationJournal: Chem.Biol.Interact / Year: 2013
Title: X-ray structure of the V301L aldo-keto reductase 1B10 complexed with NADP(+) and the potent aldose reductase inhibitor fidarestat: Implications for inhibitor binding and selectivity.
Authors: Ruiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Farres, J. / Pares, X. / Podjarny, A.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,1444
Polymers36,0861
Non-polymers1,0583
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.022, 89.022, 78.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 36085.570 Da / Num. of mol.: 1 / Mutation: V301L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Plasmid: pET30-Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FID / (2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE / FIDARESTAT / Fidarestat


Mass: 279.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10FN3O4 / Comment: inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG 6000, 100 mM SODIUM CACODYLATE , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Sep 17, 2009 / Details: OSMIC MIRRORS
RadiationMonochromator: DOUBLE MIRRORS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.597→50 Å / Num. all: 46712 / Num. obs: 46665 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 21.535 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 19.91
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.597-1.663.20.322199.8
1.66-1.723.50.241199.9
1.72-1.83.80.1811100
1.8-1.94.20.1541100
1.9-2.025.20.1371100
2.02-2.1760.1321100
2.17-2.396.90.1271100
2.39-2.748.40.1111100
2.74-3.4580.0781100
3.45-507.20.046199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
PHENIXdev_1278refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUA
Resolution: 1.5971→22.498 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 2355 5.06 %
Rwork0.1754 --
obs0.1765 46575 99.78 %
all-46678 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.0529 Å2
Refinement stepCycle: LAST / Resolution: 1.5971→22.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 69 390 3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082854
X-RAY DIFFRACTIONf_angle_d1.4143904
X-RAY DIFFRACTIONf_dihedral_angle_d13.2381085
X-RAY DIFFRACTIONf_chiral_restr0.077419
X-RAY DIFFRACTIONf_plane_restr0.006502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5971-1.62970.2551320.2292559X-RAY DIFFRACTION99
1.6297-1.66510.24661340.2192600X-RAY DIFFRACTION100
1.6651-1.70380.24391310.22062596X-RAY DIFFRACTION100
1.7038-1.74640.25621310.21092614X-RAY DIFFRACTION100
1.7464-1.79360.22491290.20662590X-RAY DIFFRACTION100
1.7936-1.84640.23031430.21212597X-RAY DIFFRACTION100
1.8464-1.9060.24591320.20952604X-RAY DIFFRACTION100
1.906-1.9740.24351480.20312598X-RAY DIFFRACTION100
1.974-2.0530.25471230.19382600X-RAY DIFFRACTION100
2.053-2.14640.22281240.19392603X-RAY DIFFRACTION100
2.1464-2.25950.18451430.19172611X-RAY DIFFRACTION100
2.2595-2.40090.21951500.19142598X-RAY DIFFRACTION100
2.4009-2.5860.18941400.18782598X-RAY DIFFRACTION100
2.586-2.84580.19991490.18282584X-RAY DIFFRACTION100
2.8458-3.25650.19131460.17192602X-RAY DIFFRACTION100
3.2565-4.09880.16331530.14592606X-RAY DIFFRACTION100
4.0988-22.49990.15921470.13822660X-RAY DIFFRACTION100

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