Table 1. Recapitulation of native active sites by ProdaMatch for ten scaffolds.
| PDB | Active site residues a | No.sites b | Rank/No.matches c | RMSD of TS d |
|---|---|---|---|---|
| 1c2t | Asn106, His108, Asp144 / Gly117, Tyr115 / Thr140, Ile91 | 44 (27) | 1/1 (20/28) | 0.24 (7.56) |
| 1dqx | Asp91, Asp273, Lys93, Lys59 / Ser35 / Ser154, Gly234, Thr277 | 29 (29) | 1/2 (37/16164) | 0.28 (1.79) |
| 1h2j | Glu225, Glu136 / His197, Tyr199 / Tyr63, Ala231, Trp259 | 24 (24) | 1/19 (39/190) | 0.42 (3.94) |
| 1jcl | Lys168, Asp103, Lys202 / Asp17, Lys138 / Cys48, Thr171, Ser239 | 33 (23) | 1/4 (56/709) | 0.14 (3.77) |
| 1ney | Glu164, His94, Lys11 / Glu96 / Gly231, Gly170 | 20 (20) | 1/5 (2/222) | 0.65 (1.73) |
| 1oex | Asp35, Asp217 / Ser38, Thr220 / Gly219, Gly78 | 21 (21) | 1/2 (4/35) | 0.28 (6.31) |
| 1p6o | Cys89, Cys92, His60, Glu62 / / Asn49, Asp153 | 18 (18) | 1/2 (10/28) | 0.66 (1.25) |
| 3vgc | Ser175, His42, Asp87 / Ser194 / Gly173 | 34 (34) | 1/2 (7/26) | 0.55 (1.75) |
| 4fua | His155, His94, His92 / / Thr43, Gly44 | 19 (19) | 1/133 (1/83) | 0.33 (2.96) |
| 6cpa | His69, Glu270, His196, Glu72 / Asp142 / Arg127 | 23 (23) | 1/4 (1/156) | 0.88 (1.47) |
a: Active site residues are classified into three groups and separated by slash. The first group represents catalytic residues, the middle group represents the residues which stabilize the catalytic residues, and the last group represents the residues which stabilize the TS. The residues in the minimal active site model correspond to those in the first group.
b: The column “No. sites” shows the number of candidate sites for complex active site model, and the numbers in the parentheses are for the minimal active site model.
c: The column “Rank/No. matches” shows the rank of the native match among all identified matches based on complex active site model, and the numbers shown in the parentheses are for minimal active site model.
d: The column “RMSD of TS” shows the RMS deviations of the matched TS based on the complex active site model from that in the crystal structures, and the values shown in the parentheses are for minimal active site model.