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Yorodumi- PDB-2pfh: Complex of Aldose Reductase with NADP+ and simaltaneously bound c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pfh | ||||||
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Title | Complex of Aldose Reductase with NADP+ and simaltaneously bound competetive inhibitors Fidarestat and IDD594. Concentration of Fidarestat in soaking solution is less than concentration of IDD594. | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE / NADP / IDD594 / 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 / 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: 0.85 Å | ||||||
Authors | Petrova, T. / Hazemann, I. / Cousido, A. / Mitschler, A. / Ginell, S. / Joachimiak, A. / Podjarny, A. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: Crystal packing modifies ligand binding affinity: The case of aldose reductase. Authors: Cousido-Siah, A. / Petrova, T. / Hazemann, I. / Mitschler, A. / Ruiz, F.X. / Howard, E. / Ginell, S. / Atmanene, C. / Van Dorsselaer, A. / Sanglier-Cianferani, S. / Joachimiak, A. / Podjarny, A. | ||||||
History |
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Remark 999 | sequence THERE IS A LEU -> ILE SEQUENCE CONFLICT AT RESIDUE 5 IN THE UNIPORT DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pfh.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pfh.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pfh ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pfh | HTTPS FTP |
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-Related structure data
Related structure data | 2pevC 2pf8C 1us0S 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
-Protein , 1 types, 1 molecules A
#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: AKR1B1, ALDR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, aldose reductase |
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-Non-polymers , 6 types, 662 molecules
#2: Chemical | ChemComp-CL / | ||
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#3: Chemical | ChemComp-NDP / | ||
#4: Chemical | ChemComp-LDT / | ||
#5: Chemical | ChemComp-FID / ( | ||
#6: Chemical | #7: 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: 42.77 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 Details: micro-seeding, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65255 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2006 |
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: 0.85→50 Å / Num. all: 253545 / Num. obs: 240860 / % possible obs: 95.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.32 |
Reflection shell | Resolution: 0.85→0.88 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.5 / % possible all: 69.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1US0 Resolution: 0.85→50 Å / Num. parameters: 35222 / Num. restraintsaints: 51858 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 406 / Occupancy sum hydrogen: 2441.21 / Occupancy sum non hydrogen: 3009.81 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→50 Å
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Refine LS restraints |
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