Solution structure of the 2nd PHD domain from Mi2b with C-terminal loop replaced by corresponding loop from WSTF

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Engineering a Protein Scaffold from a PHD Finger

Kwan, A.H.Y.Gell, D.A.Verger, A.Crossley, M.Matthews, J.M.Mackay, J.P.

(2003) Structure 11: 803-813

  • DOI: https://doi.org/10.1016/s0969-2126(03)00122-9
  • Primary Citation of Related Structures:  
    1MM2, 1MM3

  • PubMed Abstract: 

    The design of proteins with tailored functions remains a relatively elusive goal. Small size, a well-defined structure, and the ability to maintain structural integrity despite multiple mutations are all desirable properties for such designer proteins. Many zinc binding domains fit this description. We determined the structure of a PHD finger from the transcriptional cofactor Mi2beta and investigated the suitability of this domain as a scaffold for presenting selected binding functions. The two flexible loops in the structure were mutated extensively by either substitution or expansion, without affecting the overall fold of the domain. A binding site for the corepressor CtBP2 was also grafted onto the domain, creating a new PHD domain that can specifically bind CtBP2 both in vitro and in the context of a eukaryotic cell nucleus. These results represent a step toward designing new regulatory proteins for modulating aberrant gene expression in vivo.

  • Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006 Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mi2-beta(Chromodomain helicase-DNA-binding protein 4) and transcription factor WSTF61Homo sapiensMutation(s): 0 
Gene Names: CHD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q14839 (Homo sapiens)
Explore Q14839 
Go to UniProtKB:  Q14839
PHAROS:  Q14839
GTEx:  ENSG00000111642 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14839
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection