Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

Table 1 List of proteins studied.

Protein ID (unbound-bound)	Name of the protein	Number of residues	Ligand	Rmsd between the structures (Å)
3chy-1chn	CheY	128	Mg	1.39
5dfr-4dfr^	Dihydrofolate Reductase	158	Methotrexate	0.80
1ctr-1cll	Calmodulin	138	Trifluoperazine	14.4
2lao-1lst	K-, R-, Orn-Binding Protein	238	Lys	4.70
3tms-2tsc	Thymidylate Synthase	264	UMP, CB3	0.80
1hka-1rao	HPPK (kinase)	158	AMP	3.13
1bbs-1rne	Renin	326	CGP, NAG	6.16
2a6j-2a6d*	Antibody-Heavy chain	222	Dodecapeptide1	0.94
2a6j-2a6i*	Antibody-Heavy chain	222	Dodecapeptide2	1.10
2a6j-2a6k*	Antibody-Heavy chain	222	Dodecapeptide3	1.00
1oaq-1oau	Antibody-Heavy chain	121	DNP-Ser	0.62
1ocw-1oaz	Antibody-Heavy chain	121	Trx-Shear3	1.91

The first column lists the unbound and bound conformations PDB codes. The second column gives the protein description; the third column gives the residue numbers of the proteins. The fourth column lists the ligand bound to the protein. The last column provides the root mean square deviation (rmsd) between the unbound – bound structures considering the alpha carbons.
^The alignments are calculated over two stretches: 1–15 and 21–159.
* The alignments are calculated over two stretches: 1–136 and 141–222.

ISSN: 1472-6807