› 7deq

X-ray diffraction
1.03Å resolution

Lysozyme-sugar complex in D2O

Released:
DOI: 10.2210/pdb7deq/pdb
PDB entry 7deq coloured by chain, front view.
PDB entry 7deq coloured by chain, side view.
PDB entry 7deq coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Recent structural insights into the mechanism of lysozyme hydrolysis.
Tanaka I, Nishinomiya R, Goto R, Shimazaki S, Chatake T
Acta Crystallogr D Struct Biol 77 288-292 (2021)
PMID: 33645532

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132831 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Lysozyme C Chain: A
Molecule details ›
Chain: A
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

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand CL 4 x CL
Ligand NA 1 x NA
Ligand DOD 210 x DOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P43212
Unit cell:
a: 77.029Å b: 77.029Å c: 38.285Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.133 0.132 0.148

Quick links

Citations

2 citation in other articles

The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme.
Ramos et al. (2021)
1 more

1 mention without citation

Recent structural insights into the mechanism of lysozyme hydrolysis.
Tanaka et al. (2021)