4AMK

Fab fragment of antiporphrin antibody 13g10

4AMK の概要

• エントリーDOI: 10.2210/pdb4amk/pdb
• 分子名称: FAB13G10, HEAVY CHAIN, FAB13G10, LIGHT CHAIN, GLYCEROL, ... (5 entities in total)
• 機能のキーワード: immune system, 13g10, metalloporphyrin, catalytic antibody, peroxidase
• 由来する生物種: MUS MUSCULUS (HOUSE MOUSE); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 45929.55

構造登録者

Mahy, J.P.,Golinelli-Pimpaneau, B. (登録日: 2012-03-12, 公開日: 2012-10-31, 最終更新日: 2024-11-20)

主引用文献

Munoz Robles, V.,Marechal, J.,Bahloul, A.,Sari, M.,Mahy, J.,Golinelli-Pimpaneau, B.
Crystal Structure of Two Anti-Porphyrin Antibodies with Peroxidase Activity.
Plos One, 7:51128-, 2012

PubMed Abstract: We report the crystal structures at 2.05 and 2.45 Å resolution of two antibodies, 13G10 and 14H7, directed against an iron(III)-αααβ-carboxyphenylporphyrin, which display some peroxidase activity. Although these two antibodies differ by only one amino acid in their variable λ-light chain and display 86% sequence identity in their variable heavy chain, their complementary determining regions (CDR) CDRH1 and CDRH3 adopt very different conformations. The presence of Met or Leu residues at positions preceding residue H101 in CDRH3 in 13G10 and 14H7, respectively, yields to shallow combining sites pockets with different shapes that are mainly hydrophobic. The hapten and other carboxyphenyl-derivatized iron(III)-porphyrins have been modeled in the active sites of both antibodies using protein ligand docking with the program GOLD. The hapten is maintained in the antibody pockets of 13G10 and 14H7 by a strong network of hydrogen bonds with two or three carboxylates of the carboxyphenyl substituents of the porphyrin, respectively, as well as numerous stacking and van der Waals interactions with the very hydrophobic CDRH3. However, no amino acid residue was found to chelate the iron. Modeling also allows us to rationalize the recognition of alternative porphyrinic cofactors by the 13G10 and 14H7 antibodies and the effect of imidazole binding on the peroxidase activity of the 13G10/porphyrin complexes.

PubMed: 23240001
DOI: 10.1371/JOURNAL.PONE.0051128

実験手法

X-RAY DIFFRACTION (2.05 Å)