› 3vw3

X-ray diffraction
2.5Å resolution

Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct

Released:
DOI: 10.2210/pdb3vw3/pdb
PDB entry 3vw3 coloured by chain, front view.
PDB entry 3vw3 coloured by chain, side view.
PDB entry 3vw3 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab.
Yokoyama H, Mizutani R, Satow Y
Acta Crystallogr D Biol Crystallogr 69 504-12 (2013)
PMID: 23519658

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-234946 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain) Chain: L
Molecule details ›
Chain: L
Length: 217 amino acids
Theoretical weight: 23.99 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain) Chain: H
Molecule details ›
Chain: H
Length: 220 amino acids
Theoretical weight: 23.71 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 18 nucleotides
Theoretical weight: 5.64 KDa
DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 18 nucleotides
Theoretical weight: 5.4 KDa

Ligands and Environments

1 bound ligand:
Ligand NCO 1 x NCO
2 modified residues:
Ligand 64T 1 x 64T
Ligand 5PY 1 x 5PY

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P43212
Unit cell:
a: 68.43Å b: 68.43Å c: 243.658Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.247 0.247 0.29

Quick links

Citations

1 review citation

Photochemistry and Photobiology of the Spore Photoproduct: A 50-Year Journey.
Setlow et al. (2015)
3 other articles

6 mentions without citation

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