I'm just the beginner, so i apologize if the question is too trivial. I'm trying to perform receptor grid generation fro CAL-B by maestro. And it requires picking up the ligand from the structure for farther active site calculations. With other enzymes it works well, but in 1tca pdb structure it selects whole molecule every time i try to pick the ligand.
1TCA ia the apo-form of the enzyme, it does not contain a ligand, only the sugar group far from the active site. use 1TCB or 1TCC instead, the two other structures from the same publications which both contain B-octyl-glucoside as ligand
see
https://www.rcsb.org/structure/1TCA
https://www.rcsb.org/structure/1TCB
https://www.rcsb.org/structure/1TCC
You can change the setting by going in Edit>Preference>Ligand Detection
here you can set your preferences as per your need ans re-scan your protein for ligands.
Hope this will help you
Rajendra Bhadane, in the example mentioned by Kseniia Petrova , using different ligand detection preferences won't help. The group Kseniia mistook for the ligand in structure 1tca actually is an N-linked glycosylation (NAG-NAG), and as she expands the selection to everything covalently connected to the sugars, the whole protein is getting selected. The active site pocket in this structure is empty. The two alternatives I cited, 1tcb and 1tcc contain both the glycosylation and the real ligand.
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