9ANT

ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex.

Fraenkel, E.Pabo, C.O.

(1998) Nat Struct Biol 5: 692-697

  • DOI: 10.1038/1382
  • Primary Citation of Related Structures:  
    9ANT

  • PubMed Abstract: 
  • Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution ...

    Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. We have crystallized the Antennapedia homeodomain-DNA complex and solved this structure at 2.4 A resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein-DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain-DNA interactions.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTENNAPEDIA HOMEODOMAINE [auth A], F [auth B]62Drosophila melanogasterMutation(s): 1 
Gene Names: AntpCG1028
UniProt
Find proteins for P02833 (Drosophila melanogaster)
Explore P02833 
Go to UniProtKB:  P02833
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')A [auth C], C [auth E]15N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')B [auth D], D [auth F]15N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NI
      Query on NI

      Download Ideal Coordinates CCD File 
      G [auth B]NICKEL (II) ION
      Ni
      VEQPNABPJHWNSG-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.40 Å
      • R-Value Free: 0.239 
      • R-Value Work: 0.218 
      • R-Value Observed: 0.218 
      • Space Group: P 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 61.05α = 90
      b = 77.75β = 90
      c = 94.42γ = 90
      Software Package:
      Software NamePurpose
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1998-10-14
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance