Table 3.
Ligand-free structures and their corresponding ligand-bound complexes used in testing the minimal rotation hypothesis
PDB code | Resolution (Å) | Best ligand RMSD (Å) | ||||||
No. | Free | Bound | Protein/ligand complex | Free | Bound | Flexible docking | Rigid docking | Template size |
1M | 1ahc | 1ahb | Alpha-momorcharin/Formycin 5′-monophosphate | 2.0 | 2.2 | 0.94 | — | 88 |
2M | 1ajz | 1aj2 | Dihydropteroate synthase/Dihydropterine-diphosphate | 2.0 | 2.0 | 0.75 | — | 79 |
3 | 3cox | 1coy | Cholesterol oxidase/3-beta-hydroxy-5-androsten-17-one | 1.8 | 1.8 | 1.61 | — | 74 |
4 | 1gmq | 1gmr | RNAse SA/Guanosine-2′-monophosphate | 1.8 | 1.8 | 1.28 | 1.63 | 87 |
5 | 3grs | 1gra | Glutathione reductase/Glutathione disulfide | 1.5 | 2.0 | 0.69 | 1.88 | 139 |
6 | 1kem | 1kel | Catalytic antibody 28B4 FAB Fragment/AAHa | 2.2 | 1.9 | 0.46 | — | 74 |
7M | 2hvm | 1llo | Hevamine(endochitinase)/N-Acetyl-d-allosamine | 1.8 | 1.9 | 0.67 | — | 150 |
8 | 1nsb | 1nsc | Neuraminidase/N-acetyl neuraminic acid(sialic acid) | 2.2 | 1.7 | 0.40 | 0.67 | 74 |
9 | 1swa | 1swd | Streptavidin/Biotin | 2.0 | 1.9 | 0.62 | 0.67 | 37 |
10M | 2ptn | 1tps | Trypsin/Inhibitor A90720A | 1.5 | 1.9 | 0.93 | — | 143 |
11 | 1xib | 1xid | D-Xylose isomerase/L-Ascorbic acid | 1.6 | 1.7 | 2.28 | — | 45 |
12M | 1ydc | 1ydb | Carbonic anhydrase II/Acetazolamide | 2.0 | 1.9 | 1.42 | — | 50 |
13 | 2chs | 2cht | Chorismate mutase/Endo-oxabicyclic inhibitor | 1.9 | 2.2 | 1.02 | — | 39 |
14 | 2apr | 3apr | Acid proteinase/Reduced peptide inhibitor | 1.8 | 1.8 | 0.54 | — | 153 |
15 | 1tli | 3tmn | Thermolysin/VAL-TRP | 2.0 | 1.7 | 0.99 | 0.99 | 75 |
16 | 2ctv | 5cna | Concanavalin A/alpha-methyl-D-mannopyranoside | 2.0 | 2.0 | 1.99 | — | 57 |
17 | 2sga | 5sga | Proteinase A/Tetrapeptide ACE-PRO-ALA-PRO-TYR | 1.5 | 1.8 | 0.59 | 1.90 | 126 |
18M | 6taa | 7taa | Fam. 13 alpha amylase/Modified acarbose hexasaccharide | 2.1 | 2.0 | 0.82 | — | 133 |
The template sizes are given as the number of template points to indicate the differences in the sizes of the binding sites of the proteins.
a AAH = 1-[N-4′-nitrobenzyl-N-4′-carboxybutylaminomethylphosphonic acid.
M Proteins existing as biological monomers both in their ligand-free and ligand-bound states.