› 4xid

X-ray diffraction
2.7Å resolution

AntpHD with 15bp DNA duplex

Released:
DOI: 10.2210/pdb4xid/pdb
PDB entry 4xid coloured by chain, front view.
PDB entry 4xid coloured by chain, side view.
PDB entry 4xid 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-509080 (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*CP*AP*TP*TP*AP*GP*AP*G)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 15 nucleotides
Theoretical weight: 4.65 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 2 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ DW
Spacegroup: P43212
Unit cell:
a: 96.443Å b: 96.443Å c: 90.142Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.224 0.274
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

7 mentions without citation

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.
Kribelbauer et al. (2019)
6 more