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Yorodumi- PDB-2nvd: Human Aldose Reductase complexed with novel naphtho[1,2-d]isothia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nvd | ||||||
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Title | Human Aldose Reductase complexed with novel naphtho[1,2-d]isothiazole acetic acid derivative (2) | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / aldose reductase / TIM-barrel / protein-ligand 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 / 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 / retinal dehydrogenase activity / epithelial cell maturation / 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Steuber, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Evidence for a novel binding site conformer of aldose reductase in ligand-bound state Authors: Steuber, H. / Zentgraf, M. / La Motta, C. / Sartini, S. / 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 | 2nvd.cif.gz | 156.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nvd.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nvd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 2nvd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2nvd_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2nvd_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/2nvd ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nvd | HTTPS FTP |
-Related structure data
Related structure data | 2nvcC 1el3S C: citing same article (ref.) 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
#1: Protein | Mass: 35898.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hALR2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P15121, aldose reductase | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #4: 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: 2.15 Å3/Da / Density % sol: 42.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 120mM ammonium citrate, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 8, 2006 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 42162 / Num. obs: 42162 / % possible obs: 94.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1413 / Rsym value: 0.169 / % possible all: 63.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EL3 Resolution: 1.55→30 Å / Num. parameters: 26284 / Num. restraintsaints: 31907 / Cross valid method: FREE R / σ(F): 0 / σ(I): 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: 15 / Occupancy sum hydrogen: 2521 / Occupancy sum non hydrogen: 2850 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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