› 1keg

X-ray diffraction
2.4Å resolution

Antibody 64M-2 Fab complexed with dTT(6-4)TT

Released:
DOI: 10.2210/pdb1keg/pdb
PDB entry 1keg coloured by chain, front view.
PDB entry 1keg coloured by chain, side view.
PDB entry 1keg coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.
Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O
Acta Crystallogr D Biol Crystallogr 68 232-8 (2012)
PMID: 22349224

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-226642 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain) Chain: L
Molecule details ›
Chain: L
Length: 216 amino acids
Theoretical weight: 23.76 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain) Chain: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 23.68 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
5'-D(*TP*(64T)P*TP*T)-3' Chain: A
Molecule details ›
Chain: A
Length: 4 nucleotides
Theoretical weight: 1.19 KDa

Ligands and Environments

1 bound ligand:
Ligand NI 1 x NI
1 modified residue:
Ligand 64T 1 x 64T

Experiments and Validation Details

Entry percentile scores
X-ray source: MACSCIENCE
Spacegroup: P212121
Unit cell:
a: 73.567Å b: 137.274Å c: 49.615Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.201 0.268

Quick links

Citations

1 review citation

Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins.
Yokoyama et al. (2014)
4 other articles

4 mentions without citation

Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells.
Kaplinsky et al. (2014)
3 more