› 4yo0

X-ray diffraction
1.56Å resolution

Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide

Released:
DOI: 10.2210/pdb4yo0/pdb
PDB entry 4yo0 coloured by chain, front view.
PDB entry 4yo0 coloured by chain, side view.
PDB entry 4yo0 coloured by chain, top view.
Source organisms:
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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235395 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 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
Podoplanin Chains: E, F
Molecule details ›
Chains: E, F
Length: 14 amino acids
Theoretical weight: 1.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q86YL7 (Residues: 38-51; Coverage: 10%)
Gene names: GP36, PDPN, PSEC0003, PSEC0025

Ligands and Environments

1 bound ligand:
Ligand EDO 1 x EDO
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P21
Unit cell:
a: 42.18Å b: 80.01Å c: 132.52Å
α: 90° β: 96.61° γ: 90°
R-values:
R R work R free
0.181 0.179 0.214
Expression systems:
  • Mus musculus
  • Not provided

Quick links

Citations

1 review citation

Roles of Podoplanin in Malignant Progression of Tumor.
Suzuki et al. (2022)
21 other articles

5 mentions without citation

Advances in domain and subunit localization technology for electron microscopy.
Brown et al. (2019)
4 more