› 7c94

X-ray diffraction
2.84Å resolution

Crystal structure of the anti-human podoplanin antibody Fab fragment complex with glycopeptide

Released:
DOI: 10.2210/pdb7c94/pdb
PDB entry 7c94 coloured by chain, front view.
PDB entry 7c94 coloured by chain, side view.
PDB entry 7c94 coloured by chain, top view.
Source organisms:
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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212551 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
Light chain of Fab fragment Chains: A, D
Molecule details ›
Chains: A, D
Length: 220 amino acids
Theoretical weight: 24.26 KDa
Source organism: Mus musculus
Heavy chain of Fab fragment Chains: B, E
Molecule details ›
Chains: B, E
Length: 225 amino acids
Theoretical weight: 24.15 KDa
Source organism: Mus musculus
Podoplanin Chains: C, F
Molecule details ›
Chains: C, F
Length: 18 amino acids
Theoretical weight: 1.89 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q86YL7 (Residues: 67-84; Coverage: 13%)
Gene names: GP36, PDPN, PSEC0003, PSEC0025

Ligands and Environments

Carbohydrate polymer : NEW Components: A2G, GAL, SIA
Carbohydrate polymer
2 bound ligands:
Ligand PO4 4 x PO4
Ligand GOL 7 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P21
Unit cell:
a: 43.1Å b: 42.96Å c: 221.08Å
α: 90° β: 91.366° γ: 90°
R-values:
R R work R free
0.223 0.22 0.255
Expression system: Not provided

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