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- PDB-7pbb: Crystal structure of CD73 in complex with caffeine in the open form -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pbb | ||||||
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Title | Crystal structure of CD73 in complex with caffeine in the open form | ||||||
![]() | 5'-nucleotidase | ||||||
![]() | HYDROLASE / ecto-5'-nucleotidase / eN / inhibitor | ||||||
Function / homology | ![]() thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / GMP 5'-nucleotidase activity ...thymidylate 5'-phosphatase / thymidylate 5'-phosphatase activity / ADP catabolic process / 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / 7-methylguanosine nucleotidase / inhibition of non-skeletal tissue mineralization / adenosine biosynthetic process / Pyrimidine catabolism / GMP 5'-nucleotidase activity / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / AMP catabolic process / Nicotinate metabolism / Purine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / DNA metabolic process / leukocyte cell-cell adhesion / response to ATP / : / calcium ion homeostasis / Purinergic signaling in leishmaniasis infection / ATP metabolic process / negative regulation of inflammatory response / external side of plasma membrane / nucleotide binding / cell surface / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scaletti, E.R. / Strater, N. | ||||||
Funding support | 1items
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![]() | ![]() Title: Substrate binding modes of purine and pyrimidine nucleotides to human ecto-5'-nucleotidase (CD73) and inhibition by their bisphosphonic acid derivatives. Authors: Scaletti, E. / Huschmann, F.U. / Mueller, U. / Weiss, M.S. / Strater, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.2 KB | Display | ![]() |
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PDB format | ![]() | 183.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 853.7 KB | Display | ![]() |
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Full document | ![]() | 854.7 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p9nC ![]() 7p9rC ![]() 7p9tC ![]() 7pa4C ![]() 7pb5C ![]() 7pbaC ![]() 7pbyC ![]() 7pcpC ![]() 7pd9C ![]() 4h2gS 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60464.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 356 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CFF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CFF.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-DMS / | #5: Chemical | #6: Chemical | ChemComp-CFF / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking ...Details: 7 mg/mL protein concentration, 100 mM Tris pH 7.8, 10 % PEG6000, equal amounts of protein and reservoir. Following crystal formation (1-2 days), the crystals were transferred to soaking solution containing reservoir solution and 50 mM caffeine. Crystals were then transferred to cryo solution containing an additional 20 % glycerol, soaked for ~2-5 min, and flash frozen in liquid nitrogen. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→47.26 Å / Num. obs: 99458 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.072 / Rrim(I) all: 0.187 / Net I/σ(I): 7.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4h2g Resolution: 1.47→47.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.174 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.23 Å2 / Biso mean: 13.828 Å2 / Biso min: 6.48 Å2
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Refinement step | Cycle: final / Resolution: 1.47→47.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.472→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 24.122 Å / Origin y: 24.426 Å / Origin z: 22.754 Å
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