› 7c95

X-ray diffraction
2.13Å resolution

Crystal structure of the anti-human podoplanin antibody Fab fragment

Released:
DOI: 10.2210/pdb7c95/pdb
PDB entry 7c95 coloured by chain, front view.
PDB entry 7c95 coloured by chain, side view.
PDB entry 7c95 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.
Ogasawara S, Suzuki K, Naruchi K, Nakamura S, Shimabukuro J, Tsukahara N, Kaneko MK, Kato Y, Murata T
Biochem Biophys Res Commun 533 57-63 (2020)
PMID: 32921414

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-214323 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Light chain of Fab fragment Chains: A, C
Molecule details ›
Chains: A, C
Length: 220 amino acids
Theoretical weight: 24.26 KDa
Source organism: Mus musculus
Heavy chain of Fab fragment Chains: B, D
Molecule details ›
Chains: B, D
Length: 225 amino acids
Theoretical weight: 24.15 KDa
Source organism: Mus musculus

Ligands and Environments

3 bound ligands:
Ligand GOL 8 x GOL
Ligand SO4 9 x SO4
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P21
Unit cell:
a: 53.72Å b: 65.85Å c: 117.75Å
α: 90° β: 97.274° γ: 90°
R-values:
R R work R free
0.206 0.204 0.237

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