+Open data
-Basic information
Entry | Database: PDB / ID: 2dkr | ||||||
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Title | Solution structure of the PDZ domain from human Lin-7 homolog B | ||||||
Components | LIN-7 homolog B | ||||||
Keywords | PROTEIN TRANSPORT / Lin-7b / PDZ / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein localization to basolateral plasma membrane / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / Dopamine Neurotransmitter Release Cycle / RHO GTPases Activate Rhotekin and Rhophilins / neurotransmitter secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / exocytosis ...protein localization to basolateral plasma membrane / L27 domain binding / MPP7-DLG1-LIN7 complex / maintenance of epithelial cell apical/basal polarity / Dopamine Neurotransmitter Release Cycle / RHO GTPases Activate Rhotekin and Rhophilins / neurotransmitter secretion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / exocytosis / bicellular tight junction / PDZ domain binding / postsynaptic density membrane / cell-cell junction / protein transport / presynapse / basolateral plasma membrane / protein domain specific binding / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Suetake, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PDZ domain from human Lin-7 homolog B Authors: Suetake, T. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dkr.cif.gz | 511.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dkr.ent.gz | 447.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/2dkr ftp://data.pdbj.org/pub/pdb/validation_reports/dk/2dkr | 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: 9480.609 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: LIN7B, MALS2, VELI2, UNQ3116/PRO10200 / Plasmid: P050516-07 / Production host: Cell free synthesis / References: UniProt: Q9HAP6 |
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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: 1.12mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 90% H2O; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 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 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violation, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |