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- PDB-1ddm: SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ddm | ||||||
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Title | SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE | ||||||
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![]() | SIGNALING PROTEIN/TRANSFERASE / COMPLEX / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING DOMAIN (PTB) / ASYMMETRIC CELL DIVISION / SIGNALING PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation ...pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation / negative regulation of receptor recycling / glial cell migration / asymmetric neuroblast division / basal part of cell / embryonic heart tube development / Notch binding / centrosome localization / positive regulation of neurogenesis / negative regulation of neuroblast proliferation / negative regulation of Notch signaling pathway / positive regulation of endocytosis / regulation of neurogenesis / neuroblast proliferation / protein localization / cell cortex / negative regulation of gene expression / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS | ||||||
![]() | Zwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. | ||||||
![]() | ![]() Title: Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb. Authors: Zwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. #1: ![]() Title: Structure of a Numb PTB Domain-Peptide Complex Suggests a Basis for Diverse Binding Specificity Authors: Li, S.C. / Zwahlen, C. / Vincent, S.J. / McGlade, C.J. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 882.5 KB | Display | ![]() |
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PDB format | ![]() | 734.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 360 KB | Display | ![]() |
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Full document | ![]() | 622.4 KB | Display | |
Data in XML | ![]() | 57.7 KB | Display | |
Data in CIF | ![]() | 74.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 15277.424 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE BINDING DOMAIN (PTB) Source method: isolated from a genetically manipulated source Details: CELL FATE DETERMINANT PROTEIN / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1277.359 Da / Num. of mol.: 1 / Fragment: C-TERMINAL NAK 1437-1447 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-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. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 50mM / pH: 6.00 / Pressure: 1 atm / Temperature: 303 K | ||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2088 NOE, 50 DISTANCE RETRAINTS FORM HYDROGEN BONDS, 94 CHEMICAL SHIFT-DERIVED DIHEDRAL RESTRAINTS | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 150 / Conformers submitted total number: 20 |