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Yorodumi- PDB-3onc: Bond breakage and relocation of a covalently bound bromine of IDD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3onc | ||||||
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Title | Bond breakage and relocation of a covalently bound bromine of IDD594 in a complex with hAR T113A mutant after moderate radiation dose | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / radiation damage / T113A mutant / TIM barrel / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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 / L-ascorbic acid biosynthetic process / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / renal water homeostasis / epithelial cell maturation / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / electron transfer activity / carbohydrate metabolic process / negative regulation of apoptotic process / extracellular space / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.06 Å | ||||||
Authors | Koch, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.SYNCHROTRON RADIAT. / Year: 2011 Title: Radiation damage reveals promising interaction position Authors: Koch, C. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3onc.cif.gz | 163.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3onc.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 3onc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3onc ftp://data.pdbj.org/pub/pdb/validation_reports/on/3onc | HTTPS FTP |
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-Related 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: 35737.121 Da / Num. of mol.: 1 / Mutation: T113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: alr2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold / References: UniProt: P15121, aldose reductase |
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-Non-polymers , 5 types, 466 molecules
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-LDT / |
#4: Chemical | ChemComp-BR / |
#5: Chemical | ChemComp-CIT / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THIS SEQUENCE CONFLICT HAS BEEN DESCRIBED IN J BIOL CHEM 1989 SEP 5; 264(25): 14775-7 BY CHUNG S, ...THIS SEQUENCE CONFLICT HAS BEEN DESCRIBED IN J BIOL CHEM 1989 SEP 5; 264(25): 14775-7 BY CHUNG S, ET AL., PUBMED ID 2504709 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG 6000, 120mM citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 2009 / Details: silicon, Rh-coated |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→20 Å / Num. all: 133027 / Num. obs: 133027 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.048 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.06→1.08 Å / Redundancy: 6 % / Mean I/σ(I) obs: 20.3 / Rsym value: 0.098 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.06→10 Å / Num. parameters: 28313 / Num. restraintsaints: 36077 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 2475 / Occupancy sum non hydrogen: 2995.54 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.06→10 Å
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Refine LS restraints |
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