› 1zv5

X-ray diffraction
2Å resolution

Crystal structure of the variable domain of the camelid heavy-chain antibody D2-L29 in complex with hen egg white lysozyme

Released:
DOI: 10.2210/pdb1zv5/pdb
PDB entry 1zv5 coloured by chain, front view.
PDB entry 1zv5 coloured by chain, side view.
PDB entry 1zv5 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
De Genst E, Silence K, Decanniere K, Conrath K, Loris R, Kinne J, Muyldermans S, Wyns L
Proc Natl Acad Sci U S A 103 4586-91 (2006)
PMID: 16537393

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
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-208256 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysozyme C Chain: L
Molecule details ›
Chain: L
Length: 129 amino acids
Theoretical weight: 14.33 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P00698 (Residues: 19-147; Coverage: 100%)
Gene name: LYZ
Sequence domains: C-type lysozyme/alpha-lactalbumin family
Structure domains: Lysozyme
immunoglobulin heavy chain antibody variable domain Chain: A
Molecule details ›
Chain: A
Length: 130 amino acids
Theoretical weight: 14.34 KDa
Source organism: Camelus dromedarius
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P43212
Unit cell:
a: 114.073Å b: 114.073Å c: 35.673Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.239
Expression system: Escherichia coli

Quick links

Citations

106 review citations

Nanobodies: natural single-domain antibodies.
Muyldermans S. (2013)
105 more

7 mentions without citation

Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
De Genst et al. (2006)
6 more