5ZJT

Structure of AbdB/Exd complex bound to a 'Black14' DNA sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

Zeiske, T.Baburajendran, N.Kaczynska, A.Brasch, J.Palmer, A.G.Shapiro, L.Honig, B.Mann, R.S.

(2018) Cell Rep 24: 2221-2230


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein abdominal-B
A, E
84Drosophila melanogasterMutation(s): 0 
Gene Names: Abd-B
Find proteins for P09087 (Drosophila melanogaster)
Go to UniProtKB:  P09087
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Homeobox protein extradenticle
B
74Drosophila melanogasterMutation(s): 0 
Gene Names: exd
Find proteins for P40427 (Drosophila melanogaster)
Go to UniProtKB:  P40427
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*AP*TP*TP*TP*AP*TP*CP*AP*TP*GP*C)-3')C,H14Drosophila melanogaster
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*AP*AP*AP*TP*GP*AP*C)-3')D,G14Drosophila melanogaster
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.440α = 99.05
b = 45.630β = 100.37
c = 66.860γ = 114.18
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-09-19
    Type: Data collection, Database references, Structure summary