› 2dqd

X-ray diffraction
1.8Å resolution

Crystal structure of hyhel-10 FV mutant (Hy50f) complexed with hen egg lysozyme

Released:
DOI: 10.2210/pdb2dqd/pdb
PDB entry 2dqd coloured by chain, front view.
PDB entry 2dqd coloured by chain, side view.
PDB entry 2dqd coloured by chain, top view.
Source organisms:
Primary publication:
Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.
Shiroishi M, Tsumoto K, Tanaka Y, Yokota A, Nakanishi T, Kondo H, Kumagai I
J Biol Chem 282 6783-91 (2007)
PMID: 17166830

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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-132843 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 107 amino acids
Theoretical weight: 11.62 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q65ZI1 (Residues: 2-108; Coverage: 41%)
Gene names: Gm1409, Igkv5-39
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Ig heavy chain V region 36-60 Chain: H
Molecule details ›
Chain: H
Length: 114 amino acids
Theoretical weight: 12.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01823 (Residues: 1-113; Coverage: 100%)
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins
Lysozyme C Chain: Y
Molecule details ›
Chain: Y
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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P41212
Unit cell:
a: 56.24Å b: 56.24Å c: 232.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.215
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

A survey of the year 2007 literature on applications of isothermal titration calorimetry.
Bjelić et al. (2008)
2 more