› 1m7d

X-ray diffraction
2.3Å resolution

Crystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide

Released:
DOI: 10.2210/pdb1m7d/pdb
PDB entry 1m7d coloured by chain, front view.
PDB entry 1m7d coloured by chain, side view.
PDB entry 1m7d coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.
Vyas NK, Vyas MN, Chervenak MC, Johnson MA, Pinto BM, Bundle DR, Quiocho FA
Biochemistry 41 13575-86 (2002)
PMID: 12427018

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106858 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 215 amino acids
Theoretical weight: 23.72 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: A2NHM3 (Residues: 1-216; Coverage: 98%)
Gene names: Igk-C, Igkc
Sequence domains:
Structure domains: Immunoglobulins
Ig heavy chain V-III region J606 Chain: B
Molecule details ›
Chain: B
Length: 220 amino acids
Theoretical weight: 23.55 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01801 (Residues: 1-103, 104-115; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: MAG, RAE, RAM
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P43212
Unit cell:
a: 71Å b: 71Å c: 198Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.279
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Carbohydrate-binding modules: fine-tuning polysaccharide recognition.
Boraston et al. (2004)
4 more

3 mentions without citation

Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff.
Nivedha et al. (2014)
2 more