+Open data
-Basic information
Entry | Database: PDB / ID: 2eeg | ||||||
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Title | Solution Structure of PDZ domain of PDZ and LIM domain protein | ||||||
Components | PDZ and LIM domain protein 4 | ||||||
Keywords | METAL BINDING PROTEIN / pdz domain / pdz and lim domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / alpha-actinin binding / filamentous actin / stress fiber / early endosome lumen / adherens junction / Z disc ...recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / alpha-actinin binding / filamentous actin / stress fiber / early endosome lumen / adherens junction / Z disc / recycling endosome membrane / lamellipodium / actin binding / heart development / actin cytoskeleton organization / postsynaptic membrane / early endosome membrane / protein phosphatase binding / dendritic spine / cytoskeleton / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Niraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution Structure of PDZ domain of PDZ and LIM domain protein Authors: Niraula, T.N. / Tomizawa, T. / Koshiba, K. / Inoue, M. / Kigawa, 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 | 2eeg.cif.gz | 512.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eeg.ent.gz | 448.8 KB | Display | PDB format |
PDBx/mmJSON format | 2eeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2eeg ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2eeg | 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: 9604.780 Da / Num. of mol.: 1 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PDLIM4 / Plasmid: P050627-04 / References: UniProt: P50479 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 2.64mM PDZ domain U-13C,15N; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D20, 90% H2O Solvent system: 10% D20, 90% H2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
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 |