+Open data
-Basic information
Entry | Database: PDB / ID: 2agt | ||||||
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Title | Aldose Reductase Mutant Leu 300 Pro complexed with Fidarestat | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / NADP / Fidarestat | ||||||
Function / homology | Function and homology information glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / glycerol dehydrogenase (NADP+) activity / D/L-glyceraldehyde reductase / aldose reductase / C21-steroid hormone biosynthetic process / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / daunorubicin metabolic process / doxorubicin metabolic process / epithelial cell maturation / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Petrova, T. / Steuber, H. / Hazemann, I. / Cousido-Siah, A. / Mitschler, A. / Chung, R. / Oka, M. / Klebe, G. / El-Kabbani, O. / Joachimiak, A. / Podjarny, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Factorizing Selectivity Determinants of Inhibitor Binding toward Aldose and Aldehyde Reductases: Structural and Thermodynamic Properties of the Aldose Reductase Mutant Leu300Pro-Fidarestat Complex Authors: Petrova, T. / Steuber, H. / Hazemann, I. / Cousido-Siah, A. / Mitschler, A. / Chung, R. / Oka, M. / Klebe, G. / El-Kabbani, O. / Joachimiak, A. / Podjarny, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2agt.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agt.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 2agt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2agt_validation.pdf.gz | 739.5 KB | Display | wwPDB validaton report |
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Full document | 2agt_full_validation.pdf.gz | 749.2 KB | Display | |
Data in XML | 2agt_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2agt_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agt ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agt | HTTPS FTP |
-Related structure data
Related structure data | 1pwmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36164.578 Da / Num. of mol.: 1 / Mutation: L300P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15121, aldose reductase |
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-Non-polymers , 5 types, 589 molecules
#2: Chemical | ChemComp-CL / |
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#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-FID / ( |
#5: Chemical | ChemComp-CIT / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.7 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297.K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65255 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jul 24, 2004 Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65255 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. all: 163312 / Num. obs: 163149 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.057 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.51 / Rsym value: 0.386 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PWM Resolution: 1→50 Å / Num. parameters: 35133 / Num. restraintsaints: 52767 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 141 / Occupancy sum hydrogen: 2463.93 / Occupancy sum non hydrogen: 3146.63 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→50 Å
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Refine LS restraints |
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