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Table 1 List of proteins studied.

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

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
  1. 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.
  2. ^The alignments are calculated over two stretches: 1–15 and 21–159.
  3. * The alignments are calculated over two stretches: 1–136 and 141–222.