› 1nk3

Solution NMR

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE

Released:
DOI: 10.2210/pdb1nk3/pdb
PDB entry 1nk3 coloured by chain, front view.
PDB entry 1nk3 coloured by chain, side view.
PDB entry 1nk3 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA
Biochemistry 36 5372-80 (1997)
PMID: 9154919

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114256 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homeobox protein vnd Chain: P
Molecule details ›
Chain: P
Length: 77 amino acids
Theoretical weight: 9.37 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P22808 (Residues: 537-613; Coverage: 11%)
Gene names: CG6172, NK2, vnd
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 16 nucleotides
Theoretical weight: 4.96 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided
DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.84 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: DISTANCE GEOMETRY/ SIMULATED ANNEALING
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

Intrinsically disordered regions as affinity tuners in protein-DNA interactions.
Vuzman et al. (2012)
9 more

6 mentions without citation

Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components.
Privalov et al. (2011)
5 more