Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.82 kDa 
• Atom Count: 463 
• Modelled Residue Count: 61 
• Deposited Residue Count: 61 
• Unique protein chains: 1

1MM2

Solution structure of the 2nd PHD domain from Mi2b

• PDB DOI: 10.2210/pdb1MM2/pdb
• BMRB: 5555

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-09-02 Released: 2003-07-22 
• Deposition Author(s): Kwan, A.H.Y., Gell, D.A., Verger, A., Crossley, M., Matthews, J.M., Mackay, J.P.

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Experimental Data Snapshot

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

Literature

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

• PubMed: 12842043 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mi2-beta	A	61	Homo sapiens	Mutation(s): 0  Gene Names: CHD4 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14839 (Homo sapiens) Explore Q14839  Go to UniProtKB:  Q14839
PHAROS:  Q14839 GTEx:  ENSG00000111642

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1MM2 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-02 
• Released Date: 2003-07-22 
Deposition Author(s): Kwan, A.H.Y., Gell, D.A., Verger, A., Crossley, M., Matthews, J.M., Mackay, J.P.

Revision History  

• 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