+Open data
-Basic information
Entry | Database: PDB / ID: 2dm2 | ||||||
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Title | Solution structure of the first ig domain of human palladin | ||||||
Components | palladin | ||||||
Keywords | PROTEIN BINDING / beta-sandwich / KIAA0992 / myopalladin / actin-associated scaffold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dendrite self-avoidance / cell-cell adhesion mediator activity / muscle alpha-actinin binding / epithelial cell morphogenesis / podosome / keratinocyte development / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory synapse / stress fiber / cytoskeleton organization ...dendrite self-avoidance / cell-cell adhesion mediator activity / muscle alpha-actinin binding / epithelial cell morphogenesis / podosome / keratinocyte development / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory synapse / stress fiber / cytoskeleton organization / ruffle / axon guidance / actin filament / Z disc / cell migration / actin cytoskeleton / lamellipodium / actin binding / growth cone / actin cytoskeleton organization / axon / focal adhesion / mitochondrion / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first ig domain of human palladin Authors: Nagashima, 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 | 2dm2.cif.gz | 640.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dm2.ent.gz | 536.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dm2 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dm2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 11923.438 Da / Num. of mol.: 1 / Fragment: IG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KIAA0992 / Plasmid: P050711-06 / References: GenBank: 21361585, UniProt: Q8WX93*PLUS |
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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: 0.76mM uniformly 13C and 15N labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O Solvent system: 10% D2O, 90% H2O |
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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 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |