9ANT

ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 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.Mol.Biol. 5: 692-697

  • DOI: 10.1038/1382

  • 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 re ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTENNAPEDIA HOMEODOMAIN
A, B
62Drosophila melanogasterMutation(s): 1 
Gene Names: Antp
Find proteins for P02833 (Drosophila melanogaster)
Go to UniProtKB:  P02833
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3')C,E15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')D,F15N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 61.050α = 90.00
b = 77.750β = 90.00
c = 94.420γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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