+Open data
-Basic information
Entry | Database: PDB / ID: 1ndw | ||||||
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Title | Crystal Structure of Adenosine Deaminase Complexed with FR221647 | ||||||
Components | Adenosine Deaminase | ||||||
Keywords | HYDROLASE / SBDD / TIM-barrel | ||||||
Function / homology | Function and homology information negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process ...negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process / anchoring junction / T cell activation / lysosome / cell adhesion / external side of plasma membrane / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kinoshita, T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: A highly potent non-nucleoside adenosine deaminase inhibitor: efficient drug discovery by intentional lead hybridization Authors: Terasaka, T. / Kinoshita, T. / Kuno, M. / Nakanishi, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ndw.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndw.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ndw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndw ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndw | 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
#1: Protein | Mass: 40341.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: intestine / References: UniProt: P56658, adenosine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FR2 / |
#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: 2.53 Å3/Da / Density % sol: 51.42 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Ammonium phosphate, PEG400, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Kinoshita, T., (1999) Acta Crystallogr.,Sect., D55, 2031. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 30, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 29060 / Num. obs: 27869 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.039 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.216 / % possible all: 97.9 |
-Processing
Software | Name: CNX / Classification: refinement | ||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.273 | ||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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