› 2r1w

X-ray diffraction
1.7Å resolution

Crystal structure of S25-2 Fab in complex with Kdo analogues

Released:
DOI: 10.2210/pdb2r1w/pdb
PDB entry 2r1w coloured by chain, front view.
PDB entry 2r1w coloured by chain, side view.
PDB entry 2r1w 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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106907 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 219 amino acids
Theoretical weight: 24.24 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: Q52L64 (Residues: 21-240; Coverage: 100%)
Gene names: Gm10883, Igkv8-30
Sequence domains:
Structure domains: Immunoglobulins
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 222 amino acids
Theoretical weight: 24.11 KDa
Source organism: Mus musculus
UniProt:
  • Canonical: A2NU21 (Residues: 19-119; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain
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 MG 3 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-002
Spacegroup: P212121
Unit cell:
a: 45.68Å b: 81.2Å c: 131.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.219 0.246

Quick links

Citations

3 review citations

Antibody recognition of carbohydrate epitopes†.
Haji-Ghassemi et al. (2015)
2 more

1 mention without citation

Leak Proof PDBBind: A Reorganized Dataset of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction.
Li et al. (2023)