[English] 日本語
Yorodumi- PDB-3sxs: Crystal structure of BMX non-receptor tyrosine kinase complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sxs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of BMX non-receptor tyrosine kinase complexed with PP2 | ||||||
Components | Cytoplasmic tyrosine-protein kinase BMX | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / protein autophosphorylation ...phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / protein autophosphorylation / adaptive immune response / cell adhesion / intracellular signal transduction / protein phosphorylation / apoptotic process / signal transduction / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Sack, J. / Muckelbauer, J. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2011 Title: X-ray crystal structure of bone marrow kinase in the x chromosome: a Tec family kinase. Authors: Muckelbauer, J. / Sack, J.S. / Ahmed, N. / Burke, J. / Chang, C.Y. / Gao, M. / Tino, J. / Xie, D. / Tebben, A.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3sxs.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3sxs.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 3sxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxs ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxs | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31210.031 Da / Num. of mol.: 1 / Fragment: UNP residues 411-675 / Mutation: Q432K, Q611M, D617T, Q620E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGMX1, ATK, BMX, BPK, BTK / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P51813, non-specific protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-PP2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 23173 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 27.27 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→47.47 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.51 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.193 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→47.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.89→1.97 Å / Total num. of bins used: 12
|