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- PDB-5m2f: Crystal structure of human AKR1B10 complexed with NADP+ and the s... -

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Basic information

Entry
Database: PDB / ID: 5m2f
TitleCrystal structure of human AKR1B10 complexed with NADP+ and the synthetic retinoid UVI2008
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / TIM barrel / Aldo-Keto Reductase / Synthetic Retinoid / Cytosolic
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-UV8 / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsRuiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Porte, S. / Alvarez, S. / Dominguez, M. / Alvarez, R. / de Lera, A.R. / Pares, X. / Farres, J. / Podjarny, A.
CitationJournal: Chem. Biol. Interact. / Year: 2017
Title: Structural basis for the inhibition of AKR1B10 by the C3 brominated TTNPB derivative UVI2008.
Authors: Ruiz, F.X. / Crespo, I. / Alvarez, S. / Porte, S. / Gimenez-Dejoz, J. / Cousido-Siah, A. / Mitschler, A. / de Lera, A.R. / Pares, X. / Podjarny, A. / Farres, J.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,6804
Polymers36,4471
Non-polymers1,2333
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-2 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.475, 79.475, 49.823
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: 36447.121 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-UV8 / 3-bromo-4-[(1E)-2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)prop-1-en-1-yl]benzoic acid


Mass: 427.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27BrO2
#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.: 118 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 16, 2013
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 55875 / % possible obs: 99.66 % / Redundancy: 2.6 % / Rsym value: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.22

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Processing

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

1zua


Resolution: 1.503→40.359 Å / Cross valid method: FREE R-VALUE / σ(F): 2.69 / Phase error: 24.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2890 5.17 %Random 5%
Rwork0.21 ---
obs0.212 55875 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.503→40.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 79 118 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072768
X-RAY DIFFRACTIONf_angle_d1.1753768
X-RAY DIFFRACTIONf_dihedral_angle_d14.4981086
X-RAY DIFFRACTIONf_chiral_restr0.074402
X-RAY DIFFRACTIONf_plane_restr0.005469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5026-1.52850.22811560.26482562X-RAY DIFFRACTION93
1.5285-1.55630.23281280.24572687X-RAY DIFFRACTION95
1.5563-1.58620.2361570.252600X-RAY DIFFRACTION94
1.5862-1.61860.23921420.24732660X-RAY DIFFRACTION94
1.6186-1.65370.2411500.25462641X-RAY DIFFRACTION95
1.6537-1.69220.22771700.25072606X-RAY DIFFRACTION93
1.6922-1.73450.25291000.2512704X-RAY DIFFRACTION96
1.7345-1.78130.27761400.25952637X-RAY DIFFRACTION95
1.7813-1.83370.24181480.24692674X-RAY DIFFRACTION95
1.8337-1.89290.27161320.24982650X-RAY DIFFRACTION95
1.8929-1.96050.22411800.24022601X-RAY DIFFRACTION93
1.9605-2.03890.26471430.2312704X-RAY DIFFRACTION95
2.0389-2.13160.2481700.2342596X-RAY DIFFRACTION94
2.1316-2.24380.26371460.22932653X-RAY DIFFRACTION95
2.2438-2.38420.27991680.22662643X-RAY DIFFRACTION94
2.3842-2.56790.26411480.22922663X-RAY DIFFRACTION95
2.5679-2.82570.27161480.22752651X-RAY DIFFRACTION95
2.8257-3.2330.27381220.20082671X-RAY DIFFRACTION96
3.233-4.06750.2031320.16492680X-RAY DIFFRACTION95
4.0675-19.87050.18861100.15822681X-RAY DIFFRACTION96

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