› 6jb8

X-ray diffraction
1.65Å resolution

Crystal structure of nanobody D3-L11 in complex with hen egg-white lysozyme

Released:
DOI: 10.2210/pdb6jb8/pdb
PDB entry 6jb8 coloured by chain, front view.
PDB entry 6jb8 coloured by chain, side view.
PDB entry 6jb8 coloured by chain, top view.
Source organisms:
Primary publication:
Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.
Akiba H, Tamura H, Kiyoshi M, Yanaka S, Sugase K, Caaveiro JMM, Tsumoto K
Sci Rep 9 15481 (2019)
PMID: 31664051

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 analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208282 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nanobody D3-L11 Chain: A
Molecule details ›
Chain: A
Length: 136 amino acids
Theoretical weight: 14.84 KDa
Source organism: Camelus dromedarius
Expression system: Escherichia coli
Lysozyme C Chain: B
Molecule details ›
Chain: B
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

Ligands and Environments

4 bound ligands:
Ligand NO3 1 x NO3
Ligand NA 3 x NA
Ligand GOL 2 x GOL
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 40.24Å b: 49.48Å c: 59.28Å
α: 90° β: 93.4° γ: 90°
R-values:
R R work R free
0.17 0.169 0.207
Expression system: Escherichia coli

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Citations

2 review citations

Ancient species offers contemporary therapeutics: an update on shark VNAR single domain antibody sequences, phage libraries and potential clinical applications.
English et al. (2020)
1 more

2 mentions without citation

Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.
Akiba et al. (2019)
1 more