[English] 日本語
![](img/lk-miru.gif)
- PDB-5vep: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB S... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5vep | ||||||
---|---|---|---|---|---|---|---|
Title | MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F | ||||||
![]() | Kynurenine--oxoglutarate transaminase 3 | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE III / MOUSE / RE-REFINEMENT | ||||||
Function / homology | ![]() cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process ...cysteine-S-conjugate beta-lyase activity / L-kynurenine catabolic process / kynurenine-glyoxylate transaminase activity / kynurenine-glyoxylate transaminase / cysteine-S-conjugate beta-lyase / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / kynurenine metabolic process / 2-oxoglutarate metabolic process / amino acid metabolic process / biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wlodawer, A. / Dauter, Z. / Minor, W. / Stanfield, R. / Porebski, P. / Jaskolski, M. / Pozharski, E. / Weichenberger, C.X. / Rupp, B. | ||||||
![]() | Journal: Mol. Cell. Biol. / Year: 2009 Title: Biochemical and structural properties of mouse kynurenine aminotransferase III. Authors: Han, Q. / Robinson, H. / Cai, T. / Tagle, D.A. / Li, J. | ||||||
History |
| ||||||
Remark 0 | This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R. ...This entry reflects an alternative modeling of the original data in 3E2F, determined by Q.HAN,R.ROBINSON,T.CAI,D.A.TAGLE,J.LI | ||||||
Remark 200 | SEE THE ORIGINAL DATA, ENTRY 3E2F | ||||||
Remark 280 | SEE THE ORIGINAL DATA, ENTRY 3E2F |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 493.1 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vehC ![]() 5veqC ![]() 5verC ![]() 5vetC ![]() 5vf2C ![]() 5vf5C ![]() 5vgaC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46453.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q71RI9, kynurenine-oxoglutarate transaminase, cysteine-S-conjugate beta-lyase, kynurenine-glyoxylate transaminase |
---|
-Non-polymers , 5 types, 176 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.59 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% PEG 400, 150 MM CACL2, 10%, GLYCEROL, 100 MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→29.21 Å / Num. obs: 29301 / % possible obs: 91.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.57 Å2 / Biso mean: 36.919 Å2 / Biso min: 14.52 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.59→29.21 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.592→2.658 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|