+Open data
-Basic information
Entry | Database: PDB / ID: 3lbo | ||||||
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Title | Human aldose reductase mutant T113C complexed with IDD594 | ||||||
Components | Aldose reductase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Tim barrel / T113C mutant oxidoreductase / NADP / Phosphoprotein / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.1 Å | ||||||
Authors | Koch, C. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Tracing the detail: how mutations affect binding modes and thermodynamic signatures of closely related aldose reductase inhibitors 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 | 3lbo.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lbo.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lbo_validation.pdf.gz | 1020.4 KB | Display | wwPDB validaton report |
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Full document | 3lbo_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3lbo_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3lbo_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/3lbo ftp://data.pdbj.org/pub/pdb/validation_reports/lb/3lbo | HTTPS FTP |
-Related structure data
Related structure data | 3ld5C 3lepC 3lqgC 3lqlC 3lz3C 3lz5C 3m4hC C: citing same article (ref.) |
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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: 35900.379 Da / Num. of mol.: 1 / Mutation: T113C 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): Bl21 GOLD / References: UniProt: P15121, aldose reductase |
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-Non-polymers , 5 types, 417 molecules
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-LDT / |
#4: Chemical | ChemComp-CIT / |
#5: Chemical | ChemComp-BR / |
#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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG 6000, 120mM ammonium citrate, 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2008 / 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: 1.1→10 Å / Num. all: 120890 / Num. obs: 120890 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.068 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 5335 / Rsym value: 0.301 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→10 Å / Num. parameters: 28004 / Num. restraintsaints: 35650 / 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: 26 / Occupancy sum hydrogen: 2487.84 / Occupancy sum non hydrogen: 2979.65 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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