› 4xic

X-ray diffraction
2.69Å resolution

ANTPHD WITH 15BP di-thioate modified DNA DUPLEX

Released:
DOI: 10.2210/pdb4xic/pdb
PDB entry 4xic coloured by chain, front view.
PDB entry 4xic coloured by chain, side view.
PDB entry 4xic coloured by chain, top view.
Source organisms:
Primary publication:
Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J
Biophys J 109 1026-37 (2015)
PMID: 26331260

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118262 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homeotic protein antennapedia Chains: A, D
Molecule details ›
Chains: A, D
Length: 61 amino acids
Theoretical weight: 7.96 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P02833 (Residues: 297-356; Coverage: 16%)
Gene names: Antp, CG1028
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)P*AP*TP*TP*AP*GP*AP*G)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 15 nucleotides
Theoretical weight: 4.68 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NI 3 x NI
Ligand MPD 3 x MPD
1 modified residue:
Ligand C2S 2 x C2S

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 96.539Å b: 96.539Å c: 89.546Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.216 0.272
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes.
Ni et al. (2017)
5 more

3 mentions without citation

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Zandarashvili et al. (2015)
2 more