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Yorodumi- PDB-2j8t: Human aldose reductase in complex with NADP and citrate at 0.82 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j8t | ||||||
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Title | Human aldose reductase in complex with NADP and citrate at 0.82 angstrom | ||||||
Components | ALDO-KETO REDUCTASE FAMILY 1, MEMBER B1 | ||||||
Keywords | OXIDOREDUCTASE / NADP / CITRATE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 0.82 Å | ||||||
Authors | Biadene, M. / Hazemann, I. / Cousido, A. / Ginell, S. / Sheldrick, G.M. / Podjarny, A. / Schneider, T.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: The Atomic Resolution Structure of Human Aldose Reductase Reveals that Rearrangement of a Bound Ligand Allows the Opening of the Safety-Belt Loop. Authors: Biadene, M. / Hazemann, I. / Cousido, A. / Ginell, S. / Joachimiak, A. / Sheldrick, G.M. / Podjarny, A. / Schneider, T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j8t.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j8t.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 2j8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j8t ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j8t | HTTPS FTP |
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-Related structure data
Related structure data | 1el3S 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) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q5U031, UniProt: P15121*PLUS, aldose reductase | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 20.69 % |
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Crystal grow | pH: 5 Details: AS DESCRIBED IN LAMOUR ET AL. (1999) ACTA CRYSTALL. SECTION D 55: 721-723, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 10 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.7999 |
Detector | Type: ADSC CCD / Detector: CCD 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: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 0.82→34.6 Å / Num. obs: 282677 / % possible obs: 94.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 0.82→0.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 11.8 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EL3 Resolution: 0.82→34.6 Å / Num. parameters: 32154 / Num. restraintsaints: 44811 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 175 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.82→34.6 Å
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Refine LS restraints |
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