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

PDBChainSegmentsIs ReferenceOther ChainsPDB In Display
4jm2EnanoA,B4jm2EAB-tran.pdb
3ngbGnayesH,L3ngbGHL-tran.pdb
4j6rGnanoH,L4j6rGHL-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 "3ngb", chain "G" is used as reference structrue. The PDB file is named as "3ngbG.pdb" in the display window.

The input protein structures are 4jm2.pdb, 3ngb.pdb, and 4j6r.pdb. The protein structure alignment is calculated on the following chains: 4jm2:E; 3ngb:G; 4j6r:G.

4jm2:E: GP120; CORE WITH MINI V3 LOOP;
3ngb:G: ENVELOPE GLYCOPROTEIN GP160; UNP RESIDUES 43-122, 201-303, 325-486;
4j6r:G: ENVELOPE GLYCOPROTEIN GP160;
After structure superposition, other chains that are added to the superimposed structures are: 4jm2:A,B; 3ngb:H,L; 4j6r:H,L.
4jm2:A: PGT 135 HEAVY CHAIN; FAB; 4jm2:B: PGT 135 LIGHT CHAIN; FAB;
3ngb:H: ANTIGEN BINDING FRAGMENT OF HEAVY CHAIN: ANTIBODY VRC01; 3ngb:L: ANTIGEN BINDING FRAGMENT OF LIGHT CHAIN: ANTIBODY VRC01;
4j6r:H: HEAVY CHAIN OF ANTIBODY VRC23; 4j6r:L: LIGHT CHAIN OF ANTIBODY VRC23;