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Yorodumi- PDB-1kz5: Solution structure of the third helix of Antennapedia homeodomain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kz5 | ||||||
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Title | Solution structure of the third helix of Antennapedia homeodomain derivatives (RQIKIWFRKWKK) | ||||||
Components | Antennapedia protein | ||||||
Keywords | DNA BINDING PROTEIN / irregular helix and multiple turn-like structure / flexibility | ||||||
Function / homology | Function and homology information specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Authors | Czajlik, A. / Mesko, E. / Penke, B. / Perczel, A. | ||||||
Citation | Journal: J.Pept.Sci. / Year: 2002 Title: Investigation of penetratin peptides. Part 1. The environment dependent conformational properties of penetratin and two of its derivatives. Authors: Czajlik, A. / Mesko, E. / Penke, B. / Perczel, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kz5.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kz5.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kz5_validation.pdf.gz | 335.7 KB | Display | wwPDB validaton report |
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Full document | 1kz5_full_validation.pdf.gz | 408.5 KB | Display | |
Data in XML | 1kz5_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1kz5_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kz5 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kz5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1723.160 Da / Num. of mol.: 1 / Mutation: DEL(Q57,N58,R60,M61) / Source method: obtained synthetically Details: This sequence was synthetized in solid-phase using the Boc-chemistry. The sequence of this peptide is based on a sequence naturally found in Drosophila melanogaster (fruit fly). References: UniProt: P02833 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 1.5mM peptide; 90% TFEd2, 10% D2O / Solvent system: 90% TFEd2, 10% D2O |
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Sample conditions | pH: 3 / Pressure: ambient / Temperature: 300 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: the structures are based on a total of 291 NOE-derived distance restraints | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 16 |