1BAF

2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN

1BAF の概要

• エントリーDOI: 10.2210/pdb1baf/pdb
• 分子名称: IGG1-KAPPA AN02 FAB (LIGHT CHAIN), IGG1-KAPPA AN02 FAB (HEAVY CHAIN), N-(2-AMINO-ETHYL)-4,6-DINITRO-N'-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE (3 entities in total)
• 機能のキーワード: immunoglobulin, immune system
• 由来する生物種: Mus musculus (mouse); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 47613.00

構造登録者

Leahy, D.J.,Brunger, A.T.,Fox, R.O.,Hynes, T.R. (登録日: 1992-01-16, 公開日: 1994-01-31, 最終更新日: 2024-10-23)

主引用文献

Brunger, A.T.,Leahy, D.J.,Hynes, T.R.,Fox, R.O.
2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten.
J.Mol.Biol., 221:239-256, 1991

PubMed Abstract: The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was refined 2.5 A crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (gamma 1, kappa, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19.5% for 12,129 unique reflections between 8.0 and 2.9 A. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0.014 A, and the r.m.s. deviation from ideal bond angles is 3.1 degrees. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments.

PubMed: 1920408

実験手法

X-RAY DIFFRACTION (2.9 Å)