|  |  |  | sRMSD (Å) |  |
---|
Protein
|
apo
PDB
|
holo
PDB
|
ligand
|
starting
|
lowest in ensemble
|
predicted holo
|
server ID
|
RBP
|
1URP
|
1DRI
|
ribose
|
12.1
|
7.0
|
14.8
|
ce828024-27360
|
ADK
|
2AK3
|
1AK2
|
SO4
|
17.0
|
3.8
|
11.2
|
ce829841-12334
|
RBP | 1URP | 1DRI | ATP | 12.1 | 3.5 | 5.8 | ce105518-17825 |
ADK | 2AK3 | 1AK2 | ATP | 17.0 | 4.6 | 5.3 | ce131413-8235 |
GlnBP | 1GGG | 1WDN | glutamine | 15.7 | 4.2 | 5.3 | ce963091-2997 |
BC | 1ULZ | 1DV2 | ATP | 14.8 | 6.7 | 10.9 | ce889203-5498 |
MurA | 1EJD | 1A2N | T6361 | 4.9 | 4.8 | 9.0 | ce336773-19756 |
- The five proteins (RBP, ADK, GlnBP, BC, and MurA) were each submitted to CE. For each protein, the parameters of f were fitted using the results of the other four proteins. In a preliminary round we computed closure of RBP binding its natural ligand, ribose, and of ADK binding SO4 (with which it has been cocrystallized in holo form) but sRMSD of the predicted structures was high (14.8 and 11.2Ã…, italic type). In the final round of calculations these two proteins were submitted with ATP as a ligand (next two rows, regular type), resulting in much lower sRMSD. GlnBP and BC were submitted with their natural ligands, and MurA with an antibiotic.