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- PDB-4igs: Crystal structure of human Aldose Reductase complexed with NADP+ ... -

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Basic information

Entry
Database: PDB / ID: 4igs
TitleCrystal structure of human Aldose Reductase complexed with NADP+ and JF0064
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / TIM barrel / Aldose reductase / oxidoreductase / diabetes / Halogenated compound / Cytosolic / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...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 / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / metanephric collecting duct development / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / retinoid metabolic process / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / 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
2,2',3,3',5,5',6,6'-octafluorobiphenyl-4,4'-diol / 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: 0.85 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Porte, S. / de Lera, A.R. / Martin, M.J. / de la Fuente, J.A. / Klebe, G. / Farres, J. / Pares, X. / Podjarny, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design.
Authors: Cousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Porte, S. / de Lera, A.R. / Martin, M.J. / Manzanaro, S. / de la Fuente, J.A. / Terwesten, F. / Betz, M. / Klebe, G. / Farres, J. / Pares, X. / Podjarny, A.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)36,9723
Polymers35,8981
Non-polymers1,0742
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.536, 66.880, 47.525
Angle α, β, γ (deg.)90.00, 91.66, 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-64I / 2,2',3,3',5,5',6,6'-octafluorobiphenyl-4,4'-diol


Mass: 330.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H2F8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 4 IS ILE AND CORRESPONDS TO THE PROTEIN OBTAINED FROM HUMAN PLACENTA, SEE J. ...THE RESIDUE AT POSITION 4 IS ILE AND CORRESPONDS TO THE PROTEIN OBTAINED FROM HUMAN PLACENTA, SEE J. BIOL. CHEM. 264:14775-14777(1989)

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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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 6000, 100 mM MES, pH 5, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. all: 498513 / Num. obs: 498513 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.3
Reflection shellResolution: 0.85→0.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.43 / % possible all: 75.9

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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: 1US0

1us0


Resolution: 0.85→30.861 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.05 / σ(F): 1.11 / Phase error: 11.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1433 25178 5.05 %
Rwork0.1348 --
obs0.1352 498471 92.89 %
all-498471 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.261 Å2
Refinement stepCycle: LAST / Resolution: 0.85→30.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 70 638 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082973
X-RAY DIFFRACTIONf_angle_d1.4524115
X-RAY DIFFRACTIONf_dihedral_angle_d12.9351190
X-RAY DIFFRACTIONf_chiral_restr0.088453
X-RAY DIFFRACTIONf_plane_restr0.01526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.85970.22975580.229810858X-RAY DIFFRACTION64
0.8597-0.86980.22647090.215312943X-RAY DIFFRACTION76
0.8698-0.88040.21758000.207614494X-RAY DIFFRACTION85
0.8804-0.89160.20128120.194915153X-RAY DIFFRACTION89
0.8916-0.90330.18058730.177615414X-RAY DIFFRACTION91
0.9033-0.91570.16598560.162815681X-RAY DIFFRACTION92
0.9157-0.92880.16798570.146315814X-RAY DIFFRACTION93
0.9288-0.94260.14178470.137515845X-RAY DIFFRACTION93
0.9426-0.95740.14129040.130615763X-RAY DIFFRACTION93
0.9574-0.97310.13238070.127615911X-RAY DIFFRACTION94
0.9731-0.98980.11998830.119615953X-RAY DIFFRACTION94
0.9898-1.00780.12378480.116215959X-RAY DIFFRACTION94
1.0078-1.02720.13038420.11116189X-RAY DIFFRACTION95
1.0272-1.04820.1159280.105515875X-RAY DIFFRACTION95
1.0482-1.0710.11168560.102516184X-RAY DIFFRACTION95
1.071-1.09590.10718460.099316150X-RAY DIFFRACTION95
1.0959-1.12330.1138420.100716161X-RAY DIFFRACTION95
1.1233-1.15370.11618150.098116142X-RAY DIFFRACTION95
1.1537-1.18760.10838610.100316218X-RAY DIFFRACTION95
1.1876-1.2260.11038820.104516259X-RAY DIFFRACTION96
1.226-1.26980.12468420.111816389X-RAY DIFFRACTION96
1.2698-1.32060.12188570.116616535X-RAY DIFFRACTION97
1.3206-1.38070.13048470.118616439X-RAY DIFFRACTION97
1.3807-1.45350.13088350.124116627X-RAY DIFFRACTION98
1.4535-1.54460.13338720.122416641X-RAY DIFFRACTION98
1.5446-1.66380.15069610.128616575X-RAY DIFFRACTION98
1.6638-1.83130.15278570.140516736X-RAY DIFFRACTION98
1.8313-2.09620.14968450.144516715X-RAY DIFFRACTION98
2.0962-2.64080.17048390.158216540X-RAY DIFFRACTION97
2.6408-30.88170.15887970.159815130X-RAY DIFFRACTION89

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