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Yorodumi- PDB-2yub: Solution structure of the PDZ domain from mouse LIM domain kinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yub | ||||||
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Title | Solution structure of the PDZ domain from mouse LIM domain kinase | ||||||
Components | LIM domain kinase 2 | ||||||
Keywords | TRANSFERASE / PDZ domain / LIMK-2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information cornea development in camera-type eye / head development / astral microtubule organization / cis-Golgi network / mitotic spindle / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation ...cornea development in camera-type eye / head development / astral microtubule organization / cis-Golgi network / mitotic spindle / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Hayashi, F. / Suetake, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain from mouse LIM domain kinase Authors: Hayashi, F. / Suetake, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yub.cif.gz | 691.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yub.ent.gz | 598.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/2yub ftp://data.pdbj.org/pub/pdb/validation_reports/yu/2yub | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12799.146 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: Limk2 / Plasmid: P041220-03 References: UniProt: O54785, non-specific serine/threonine protein kinase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 0.47mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 1438 restraints, 1347 are NOE-derived distance constraints, 91 dihedral angle restraints. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |