A ligand in its pocket

HIV-1 protease with the inhibitor indinavir (PDB 1HSG), in four requests.

1. Open the structure

open the HIV protease structure 1hsg and show the inhibitor indinavir as orange sticks

open 1hsg
show #1:MK1 atoms; style #1:MK1 stick; color #1:MK1 orange

MK1 is the residue name of indinavir in this entry.

Indinavir as orange sticks in the middle of the protease dimer

2. The pocket as a surface

show the binding pocket: a white surface of the residues within 5 Å of indinavir, 70% transparent

surface (#1:MK1 :<5) & protein color white transparency 70

:<5 selects the residues with any atom within 5 Å of the ligand.

Transparent surface of the pocket residues around the inhibitor

3. Hydrogen bonds

show the hydrogen bonds between indinavir and the protein, and label the residues it binds

hbonds #1:MK1 restrict protein reveal true select true
select sel & protein; label sel

Nine hydrogen bonds to five residues: Arg 8, Asp 25 of both chains, Gly 27 and Asp 29. The catalytic aspartates (Asp 25) bind the inhibitor's central hydroxyl.

Hydrogen bonds drawn as dashes, with the bonded residues labelled

4. A close-up

hide the cartoon except around the pocket and give me a clean close-up of indinavir in its pocket

hide #1 target c
cartoon (#1:MK1 :<5) & protein
view #1:MK1

Indinavir, its pocket surface and the hydrogen bonds

Save figure writes the image, the session and the commands to a folder (tutorial, step 5b).