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- PDB-1kz0: Solution structure of the third helix of Antennapedia homeodomain -

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Basic information

Entry
Database: PDB / ID: 1kz0
TitleSolution structure of the third helix of Antennapedia homeodomain
ComponentsAntennapedia protein
KeywordsDNA BINDING PROTEIN / irregular helix / turn-like parts at the beginning and at the end
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 / midgut development / anterior/posterior axis specification / anterior/posterior pattern specification / 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 / midgut development / anterior/posterior axis specification / anterior/posterior pattern specification / 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
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain ...Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeotic protein antennapedia
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsCzajlik, A. / Mesko, E. / Penke, B. / Perczel, A.
CitationJournal: 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
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antennapedia protein


Theoretical massNumber of molelcules
Total (without water)2,2541
Polymers2,2541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein/peptide Antennapedia protein / penetratin


Mass: 2253.781 Da / Num. of mol.: 1 / Fragment: C-terminal fragment of Antennapedia homeodomain / Source method: obtained synthetically
Details: This sequence was synthetized in solid-phase using the Boc-chemistry. The source of this peptide is naturally found in Drosophila melanogaster (fruit fly).
References: UniProt: P02833

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.5mM peptide; 90% TFEd2, 10% D2O / Solvent system: 90% TFEd2, 10% D2O
Sample conditionspH: 3 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix97.2San Diego, MSIdata analysis
Felix97.2San Diego, MSIprocessing
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851BRUNGERstructure solution
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 553 NOE-derived restraints
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 26

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