7c94 | pdb_00007c94

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

spinqualitylabelsall models 7c94, resolution 2.84Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7c94 is a 6 chain structure with sequence from Homo sapiens and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.84Å Ligands: A2G, GAL, GOL, PO4, SIA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function PDPN_HUMAN Publication Abstract from PubMed Podoplanin (PDPN) is a highly O-glycosylated glycoprotein that is utilized as a specific lymphatic endothelial marker under pathophysiological conditions. We previously developed an anti-human PDPN (hPDPN) monoclonal antibody (mAb), clone LpMab-3, which recognizes the epitope, including both the peptides and the attached disialy-core-l (NeuAcalpha2-3Galbetal-3 [NeuAcalpha2-6]GalNAcalphal-O-Thr) structure at the Thr76 residue in hPDPN. However, it is unclear if the mAb binds directly to both the peptides and glycans. In this study, we synthesized the binding epitope region of LpMab-3 that includes the peptide (-67LVATSVNSV-T-GIRIEDLP84-) possessing a disialyl-core-1 O-glycan at Thr76, and we determined the crystal structure of the LpMab-3 Fab fragment that was bound to the synthesized glycopeptide at a 2.8 A resolution. The six amino acid residues and two sialic acid residues are directly associated with four complementarity-determining regions (CDRs; H1, H2, H3, and L3) and four CDRs (H2, H3, L1, and L3), respectively. These results suggest that IgG is advantageous for generating binders against spacious epitopes such as glycoconjugates. 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. 2020 Sep 10. pii: S0006-291X(20)31702-2. doi:, 10.1016/j.bbrc.2020.08.103. PMID:32921414 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Antibody 3D structures Monoclonal Antibodies 3D structures

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