igg1: Human immunoglobulin G1 antibody molecule
In loon.data: Data Used to Illustrate 'Loon' Functionality

Description Format Author(s) References See Also

Human immunoglobulin G1 is an antibody molecule of 10,401 atoms. The great bulk of these form residues attached to 1,556 alpha carbons (alpha refers to the first carbon that attaches to a functional group). In this protein molecule, the functional groups called residues are either amino acids or carbohydrates (sugar molecules).

On the geometry of this protein, from Padlan (1994, p. 172): "An antibody molecule is composed of three major fragments: the two Fabs, which are identical and each of which contains the light chain and the first two domains of the heavy chain, and the Fc, which contains the C-terminal constant domains of the two heavy chains. The Fabs are linked to the Fc by the hinge region, which varies in length and flexibility in the different antibody classes and isotypes. The antigen binding sites (paratopes) are located at the tips of the Fabs."

Full names for amino acid residues and group characteristics were taken from the commercial website www.tocris.com.

The data records all 1,556 alpha carbons, their residues, which of five separate chains each carbon belongs to, and the geometric location given by coordinates x, y, and z as determined by X-ray crystallography and as available to Padlan (1994) either from the Protein Data Bank or or from original investigators at the time of publication.

From the source website: "It is a composite model built from F(ab)2 fragments from Brookhaven file 2IG2.PDB, and an Fc fragment from Brookhaven file 1FC2.PDB. Part of the hinge region and other details are theoretically modeled."

A data frame with 1556 rows and 10 variates:

recordType: Either 'ATOM' or 'HETATM'. Here 'ATOM' indicates an atom having a standard residue of the protein; 'HETATM' (hetero atom) indicates one either having a non-standard residue of protein, or one in a group of a different kind such as carbohydrates, substrates, ligands, solvent, or metal ions. In the igg1 molecule, these will be a part of some carbohydrate.
name: Name of the alpha carbon atom.
residue: The three letter abbreviated name of the residue.
chainID: Chains H and I (heavy), residues 1-452 each; Chains L, and M (light), residues 501-716; Chain C (carbohydrate), residues 1-9, 10-18.
residueSequenceNum: Order in which that carbon atom appears in its chain.
x, y, z: Coordinates of the carbon atom in three-dimensonal space.
residueName: Full name of the residue.
group: A group characteristic for that residue.

R.W. Oldford

Eduardo A. Padlan (1994) "Anatomy of the Antibody Molecule", Molecular Immunology, 31, Issue 3, pp. 169 - 217.

Lisa J. Harris, Steven B. Larson, Karl W. Hasel, John Day, Aaron Greenwood and Alexander McPherson (1992) "The three-dimensional structure of an intact monoclonal antibody for canine lymphoma", Nature, 360, pp. 369-372.

elements SCmolecule

loon.data documentation built on May 14, 2021, 1:06 a.m.