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Open data
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Basic information
Entry | Database: PDB / ID: 5w4e | ||||||
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Title | Importin binding to Tdt NLS peptide | ||||||
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![]() | PROTEIN BINDING / importin / NLS / Tdt / Nuclear Transport | ||||||
Function / homology | ![]() DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / arginine metabolic process / DNA modification / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / arginase / arginase activity / positive regulation of viral life cycle / urea cycle ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / arginine metabolic process / DNA modification / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / arginase / arginase activity / positive regulation of viral life cycle / urea cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / DNA metabolic process / response to ATP / NLS-bearing protein import into nucleus / euchromatin / nuclear matrix / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / DNA-directed DNA polymerase activity / glutamatergic synapse / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pedersen, L.C. / London, R. | ||||||
![]() | ![]() Title: Variations in nuclear localization strategies among pol X family enzymes. Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.8 KB | Display | ![]() |
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PDB format | ![]() | 77 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.4 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w4fC ![]() 6d7mC ![]() 6d7nC ![]() 5e6qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55330.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: Kpna2, Rch1 / Production host: ![]() ![]() | ||||
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#2: Protein/peptide | Mass: 1838.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NLS peptide for human DNA repair polymerase Tdt / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 0.7 M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 36690 / % possible obs: 97.3 % / Redundancy: 6.7 % / Rsym value: 0.071 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.328 / % possible all: 76.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E6Q Resolution: 2.18→40.864 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 19.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→40.864 Å
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Refine LS restraints |
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LS refinement shell |
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