The protein structure alignment is based on protein structures defined as below:

PDBChainSegmentsIs ReferenceOther ChainsPDB In Display
2ny7HnayesG,L2ny7HGL-tran.pdb
3u7yHnanoG,L3u7yHGL-tran.pdb

The protein structure comparison is conducted on the defined Segments (if not "NA") from the given Chain in the protein structure defined in PDB column(could be PDB id or PDB file uploaded by the web user). If Segments is "NA", then the whole chain from column Chain is used for structure comparison. After the structures are superimposed on the selected segments from selected Chain, then Other Chains are added to the superimposed structures by structure transformation. PDB files in column PDB In Display are the result of the structure transformation and are the final PDB files in the structure display windows.

If a reference structure is defined, then all selected Segments from selected Chain from other PDBs are superimposed onto the selected Segments from the selected Chain in the reference structure.Here protein structure "2ny7", chain "H" is used as reference structrue. The PDB file is named as "2ny7H.pdb" in the display window.

The input protein structures are 2ny7.pdb, and 3u7y.pdb. The protein structure alignment is calculated on the following chains: 2ny7:H; 3u7y:H.

2ny7:H: ANTIBODY B12, HEAVY CHAIN; ANTIGEN-BINDING FRAGMENT, FAB;
3u7y:H: NIH45-46 HEAVY CHAIN, IG GAMMA-1 CHAIN C REGION;
After structure superposition, other chains that are added to the superimposed structures are: 2ny7:G,L; 3u7y:G,L.
2ny7:G: ENVELOPE GLYCOPROTEIN GP120; CORE; 2ny7:L: ANTIBODY B12, LIGHT CHAIN; ANTIGEN-BINDING FRAGMENT, FAB;
3u7y:G: ENVELOPE GLYCOPROTEIN GP160; GP120 CORE (UNP RESIDUES 43-122, 201-303, 325-486); 3u7y:L: NIH45-46 LIGHT CHAIN, IG KAPPA CHAIN C REGION;