+Open data
-Basic information
Entry | Database: PDB / ID: 4u58 | ||||||
---|---|---|---|---|---|---|---|
Title | IMPORTIN-ALPHA MINOR NLS SITE INHIBITOR | ||||||
Components | Importin subunit alpha-1 | ||||||
Keywords | TRANSPORT PROTEIN / TPX2 inhibitor | ||||||
Function / homology | Function and homology information Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.56 Å | ||||||
Authors | Stewart, M. / Valkov, E. / Holvey, R.S. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: Selective Targeting of the TPX2 Site of Importin-alpha Using Fragment-Based Ligand Design. Authors: Holvey, R.S. / Valkov, E. / Neal, D. / Stewart, M. / Abell, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4u58.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4u58.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u58_validation.pdf.gz | 702.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4u58_full_validation.pdf.gz | 705.5 KB | Display | |
Data in XML | 4u58_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 4u58_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/4u58 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/4u58 | HTTPS FTP |
-Related structure data
Related structure data | 4u54C 4u5lC 4u5nC 4u5oC 4u5sC 4u5uC 4u5vC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 46143.828 Da / Num. of mol.: 1 / Fragment: UNP residues 72-497 Source method: isolated from a genetically manipulated source Details: deltaIBB / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 |
---|---|
#2: Chemical | ChemComp-3C6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.68 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: see publication |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9686 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→62.4 Å / Num. obs: 23793 / % possible obs: 97.5 % / Redundancy: 5.3 % / Net I/σ(I): 13.5 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.56→62.311 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 109.25 Å2 / Biso mean: 45.0848 Å2 / Biso min: 19.51 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.56→62.311 Å
|