› 3bpc

X-ray diffraction
1.85Å resolution

co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo

Released:
DOI: 10.2210/pdb3bpc/pdb
PDB entry 3bpc coloured by chain, front view.
PDB entry 3bpc coloured by chain, side view.
PDB entry 3bpc coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
Brooks CL, Müller-Loennies S, Brade L, Kosma P, Hirama T, MacKenzie CR, Brade H, Evans SV
J Mol Biol 377 450-68 (2008)
PMID: 18272175

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-213223 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab, antibody fragment (IgG1k), light chain Chain: A
Molecule details ›
Chain: A
Length: 219 amino acids
Theoretical weight: 24.24 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
Fab, antibody fragment (IgG1k), heavy chain Chain: B
Molecule details ›
Chain: B
Length: 222 amino acids
Theoretical weight: 24.11 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: KDA, KDB
Ligand KDA 1 x KDA
Ligand KDB 1 x KDB
2 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 45.85Å b: 81.29Å c: 132.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.273

Quick links

Citations

3 review citations

Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
Rich et al. (2010)
2 more

1 mention without citation

Predicting binding sites from unbound versus bound protein structures.
Clark et al. (2020)