› 5jlw

X-ray diffraction
2.09Å resolution

AntpHD with 15bp DNA duplex R-monothioated at Cytidine-8

Released:
DOI: 10.2210/pdb5jlw/pdb
PDB entry 5jlw coloured by chain, front view.
PDB entry 5jlw coloured by chain, side view.
PDB entry 5jlw coloured by chain, top view.
Source organisms:
Primary publication:
Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Nguyen D, Zandarashvili L, White MA, Iwahara J
Chembiochem 17 1636-42 (2016)
PMID: 27271797

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-118875 (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*(C7R)P*AP*TP*TP*AP*GP*AP*G)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 15 nucleotides
Theoretical weight: 4.67 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 6 x NI
Ligand MPD 3 x MPD
1 modified residue:
Ligand C7R 2 x C7R

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER D8 QUEST
Spacegroup: P2221
Unit cell:
a: 61.266Å b: 75.888Å c: 93.696Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.218 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

The growth of siRNA-based therapeutics: Updated clinical studies.
Zhang et al. (2021)
1 more

3 mentions without citation

Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Nguyen et al. (2016)
2 more