2HDD

ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb2HDD/pdb
• NAKB: 2HDD

• Classification: TRANSCRIPTION/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-02-10 Released: 1998-05-27 
• Deposition Author(s): Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.

Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T., Pabo, C.O.

(1997) Structure 5: 1047-1054

• PubMed: 9309220 
• DOI: https://doi.org/10.1016/s0969-2126(97)00256-6
• Primary Citation of Related Structures:  
  2HDD


• PubMed Abstract: 
  

  The homeodomain is one of the key DNA-binding motifs used in eukaryotic gene regulation, and homeodomain proteins play critical roles in development. The residue at position 50 of many homeodomains appears to determine the differential DNA-binding specificity, helping to distinguish among binding sites of the form TAATNN. However, the precise role(s) of residue 50 in the differential recognition of alternative sites has not been clear. None of the previously determined structures of homeodomain-DNA complexes has shown evidence for a stable hydrogen bond between residue 50 and a base, and there has been much discussion, based in part on NMR studies, about the potential importance of water-mediated contacts. This study was initiated to help clarify some of these issues.

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Organizational Affiliation: 

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge 02139, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.74 kDa 
• Atom Count: 1,990 
• Modelled Residue Count: 153 
• Deposited Residue Count: 164 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ENGRAILED HOMEODOMAIN Q50K)	C [auth A], D [auth B]	61	Drosophila melanogaster	Mutation(s): 1
UniProt
Find proteins for P02836 (Drosophila melanogaster) Explore P02836  Go to UniProtKB:  P02836

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)-3')	A [auth C]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')	B [auth D]	21	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  2HDD	Kd: 8.80e-3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.72	α = 90
b = 45.34	β = 119.53
c = 72.47	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T., Pabo, C.O.

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-02-14
  Changes: Data collection