+
Open data
-
Basic information
Entry | Database: PDB / ID: 2z7g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of adenosine deaminase ligated with EHNA | ||||||
![]() | Adenosine deaminase | ||||||
![]() | HYDROLASE / beta barrel / protein-inhibitor complex / Acetylation / Nucleotide metabolism / Pharmaceutical / Polymorphism | ||||||
Function / homology | ![]() negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / inosine biosynthetic process / 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 / cytoplasmic vesicle lumen / inosine biosynthetic process / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kinoshita, T. | ||||||
![]() | ![]() Title: Conformational change of adenosine deaminase during ligand-exchange in a crystal Authors: Kinoshita, T. / Tada, T. / Nakanishi, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 85.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1krmS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40341.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-EH9 / ( |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ADA_BOVIN. GLN 196, THR 243, AND ARG 349 ARE ...THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ADA_BOVIN. GLN 196, THR 243, AND ARG 349 ARE VARIANTS OF ADA_BOVIN. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.77 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2M Ammonium sulfate, 2% MPD, 0.1M MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 31, 2007 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→67.03 Å / Num. all: 14440 / Num. obs: 13675 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.52→2.75 Å / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 3.7 / % possible all: 94.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1KRM Resolution: 2.52→67.03 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→67.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.52→2.57 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.251 |