1SKN

THE BINDING DOMAIN OF SKN-1 IN COMPLEX WITH DNA: A NEW DNA-BINDING MOTIF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new DNA-binding motif in the Skn-1 binding domain-DNA complex.

Rupert, P.B.Daughdrill, G.W.Bowerman, B.Matthews, B.W.

(1998) Nat.Struct.Mol.Biol. 5: 484-491


  • PubMed Abstract: 
  • The DNA-binding domain of Skn-1, a developmental transcription factor that specifies mesoderm in C. elegans, is shown by X-ray crystallography to have a novel fold in which a compact, monomeric, four-helix unit organizes two DNA-contact elements. At ...

    The DNA-binding domain of Skn-1, a developmental transcription factor that specifies mesoderm in C. elegans, is shown by X-ray crystallography to have a novel fold in which a compact, monomeric, four-helix unit organizes two DNA-contact elements. At the C-terminus, a helix extends from the domain to occupy the major groove of DNA in a manner similar to bZip proteins. Skn-1, however, lacks the leucine zipper found in all bZips. Additional contacts with the DNA are made by a short basic segment at the N-terminus of the domain, reminiscent of the 'homeodomain arm'.


    Organizational Affiliation

    Institute of Molecular Biology, Department of Chemistry, University of Oregon, Eugene 97403, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-BINDING DOMAIN OF SKN-1
P
92Caenorhabditis elegansMutation(s): 0 
Gene Names: skn-1
Find proteins for P34707 (Caenorhabditis elegans)
Go to UniProtKB:  P34707
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*CP*AP*AP*TP*GP*TP*CP*AP*TP*CP*CP*C)-3')A15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*GP*GP*AP*TP*GP*AP*CP*AP*TP*TP*GP*T)-3')B15N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LDA
Query on LDA

Download SDF File 
Download CCD File 
P
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.337 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.130α = 90.00
b = 93.390β = 90.00
c = 53.450γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-24
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance