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Open data
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Basic information
Entry | Database: PDB / ID: 1s1d | ||||||
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Title | Structure and protein design of human apyrase | ||||||
![]() | apyrase | ||||||
![]() | HYDROLASE / ADPase / five-blade beta propeller / calcium-binding protein / nucleotide-binding motif | ||||||
Function / homology | ![]() nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen ...nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M. | ||||||
![]() | ![]() Title: Structure and protein design of a human platelet function inhibitor. Authors: Dai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158.2 KB | Display | ![]() |
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PDB format | ![]() | 121.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s18SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37042.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 664 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GP2.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GP2.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | ChemComp-TRS / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.78 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG MME 2000, sodium acetate, ammonium sulfate, strontium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.6 Å / Num. all: 79084 / Num. obs: 79084 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7743 / % possible all: 93.8 |
Reflection | *PLUS Highest resolution: 1.6 Å |
Reflection shell | *PLUS % possible obs: 93.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S18 Resolution: 1.6→46.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.685 / SU ML: 0.059 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.089
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.372 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→46.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.634 Å / Total num. of bins used: 20
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Refinement | *PLUS Num. reflection obs: 79084 / % reflection Rfree: 5 % / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.164 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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