› 4yny

X-ray diffraction
1.58Å resolution

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1

Released:
DOI: 10.2210/pdb4yny/pdb
PDB entry 4yny coloured by chain, front view.
PDB entry 4yny coloured by chain, side view.
PDB entry 4yny coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Tailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state.
Fujii Y, Matsunaga Y, Arimori T, Kitago Y, Ogasawara S, Kaneko MK, Kato Y, Takagi J
J Cell Sci 129 1512-22 (2016)
PMID: 26872787

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235435 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Heavy chain of antigen binding fragment, Fab Chains: A, C
Molecule details ›
Chains: A, C
Length: 238 amino acids
Theoretical weight: 25.56 KDa
Source organism: Rattus norvegicus
Expression system: Mus musculus
Structure domains: Immunoglobulins
Light chain of antigen binding fragment, Fab Chains: B, D
Molecule details ›
Chains: B, D
Length: 233 amino acids
Theoretical weight: 25.49 KDa
Source organism: Rattus norvegicus
Expression system: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1, PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P1
Unit cell:
a: 42.883Å b: 57.157Å c: 101.52Å
α: 97.92° β: 101.53° γ: 105.37°
R-values:
R R work R free
0.17 0.168 0.204
Expression system: Mus musculus

Quick links

Citations

2 review citations

Roles of Podoplanin in Malignant Progression of Tumor.
Suzuki et al. (2022)
1 more

2 mentions without citation

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Guest et al. (2021)
1 more