Table 2.
Recapitulation of PAM-interacting amino acids by UniDesign with PDB PAMs
| Cas | PDB | Redesigned PIAA residue types | Recovery | Similarity |
|---|---|---|---|---|
| SpCas9 | 4UN3 | K1107K, E1219E, R1333R, R1335R | 4/4 | 4/4 |
| 5F9R | K1107K, E1219E, R1333R, R1335R | 4/4 | 4/4 | |
| SaCas9 | 5AXW | N985N, N986N, L989L, R991R, R1002K, R1015R | 5/6 | 6/6 |
| 5CZZ | N985N, N986N, L989H, R991R, R1002K, R1015R | 4/6 | 5/6 | |
| St1Cas9 | 6M0W | F673Y, T1048T, M1049Q, Y1055Y, S1082S, Q1084Q, K1086Q | 4/7 | 5/7 |
| FnCas9 | 5B2O | R1241R, E1449N, D1472D, S1473S, R1474R, S1555S, R1556R, R1585R, Y1586Y | 8/9 | 8/9 |
| Nme1Cas9 | 6JDV | Q981Q, H1024H, T1027S, N1029T, E1048E, G1049G | 4/6 | 5/6 |
| Nme2Cas9 | 6JE3 | K843K, D1028E, R1033R, Y1035W, K1044K | 3/5 | 5/5 |
| CdCas9 | 6JOO | I47R, K818K, F1011F, K1015Q, R1017R, R1042K, P1043E, L1046L | 4/8 | 5/8 |
| AceCas9 | 6WBR | R55R, E1044E, R1048R, R1088R, R1091R | 5/5 | 5/5 |
| AsCas12a | 5B43 | T167S, T539Q, K548R, P599P, K603K, M604M, K607K | 4/7 | 6/7 |
| LbCas12a | 5XUS | T149T, Q529Q, K538K, Y542Y, P587P, K591Q, M592M, K595K | 7/8 | 7/8 |
| Total | N/A | N/A | 48(47)/65 | 56(55)/65 |
Only one scaffold for SpCas9 and SaCas9 was counted for calculating the total recovery and similarity rates. The values outside and inside the parentheses were obtained with scaffold 5AXW or 5CZZ counted, respectively.