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- PDB-1eko: PIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1eko
TitlePIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE / ALDOSE REDUCTASE / INHIBITION / DIABETES
Function / homology
Function and homology information


glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase activity / allyl-alcohol dehydrogenase / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / retinal dehydrogenase activity / retinoid metabolic process ...glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase activity / allyl-alcohol dehydrogenase / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / retinal dehydrogenase activity / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / cytoplasm
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-I84 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPodjarny, A.
Citation
#1: Journal: J.AM.SOC.MASS.SPECTROM. / Year: 1999
Title: Binding of Aldose Reductase Inhibitors: Correlation of Crystallographic and Mass Spectrometric Studies
Authors: Rogniaux, H. / Van Dorsselaer, A. / Barth, P. / Biellmann, J.F. / Barbanton, J. / van Zandt, M. / Chevrier, B. / Howard, E. / Mitschler, A. / Potier, N. / Urzhumtseva, L. / Moras, D. / Podjarny, A.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9583
Polymers35,8241
Non-polymers1,1342
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.810, 68.810, 154.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ALDOSE REDUCTASE /


Mass: 35824.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: EYE / Tissue: LENS / References: UniProt: P80276, aldose reductase
#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-I84 / [2,6-DIMETHYL-4-(2-O-TOLYL-ACETYLAMINO)-BENZENESULFONYL]-GLYCINE / INHIBITOR IDD 384


Mass: 390.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 6 MG/ML AR, 2.5% PEG 6000, 25 MM MESPH 6.2 (DROP), 20% PEG 6000, 25 MM MESPH 6.2 (RESERVOIR) , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Details: Rogniaux, H., (1999) J. Am. Soc. Mass Spectrom., 10, 635.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
3NADP+1drop
475 mMMES1drop
51 mMEDTA1drop
61 mMdithiothreitol1drop
72.5 %(w/v)PEG60001drop
825 %PEG60001reservoir
91
21
101

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 20372 / Num. obs: 19184 / % possible obs: 98.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.245 / % possible all: 97.5

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALDOSE REDUCTASE NATIVE

Resolution: 2.2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 18314069.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1801 9.8 %RANDOM
Rwork0.216 ---
all0.221 20372 --
obs0.216 18338 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.8234 Å2 / ksol: 0.382389 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.42 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 75 71 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_mcbond_it1.981.5
X-RAY DIFFRACTIONx_mcangle_it3.122
X-RAY DIFFRACTIONx_scbond_it3.332
X-RAY DIFFRACTIONx_scangle_it4.822.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.394 240 11 %
Rwork0.355 1950 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PARAMTOPHCSDX_PLUS.PRO
X-RAY DIFFRACTION2NADP.PARAMNADP.TOPOL
X-RAY DIFFRACTION3I0384.PARAMI0384.TOPOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.394 / % reflection Rfree: 11 % / Rfactor Rwork: 0.355

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