# PyMOL script - serine proteases
# elastase_acyl_intermediate.pml
# jdc 2014_10_27

load 1hax.pdb, ela

# only resi 4-7 are visible in substrate
select substrate, chain A
# chain B is the elastase polypeptide
select enz, chain B
select ela-acyl, chain A | chain B
#
# these are the usual suspects:
select 190s, resi 191-195
select S195, resi 195
select H57, resi 57
select D102, resi 102
select oxyhole, resi 193-195

select waters-all, resn HOH
select wat1, resi 2032
select wat2, resi 2001
select Ca, resn CA
select SO4, resn SO4

hide everything
util.cbac substrate
util.cbag enz

# add hydrogen bonds between selections
h_add H57
select SD, S195 | D102
select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (H57 and acc),(SD and don), 3.2
dist HBD, (H57 and don),(SD and acc), 3.2
delete don
delete acc
hide (hydro)

dist HD, /ela//B/57/ND1, /ela//B/102/OD2

hide (hydro)

hide labels,HBA
hide labels,HBD

# create additional distance measurements

distance His57-water, /ela//B/2032/o, /ela//B/57/NE2

distance acyl-water, /ela//B/2032/o, /ela//A/7/c

distance oxyanion1, /ela//A/7/o, /ela//B/193/n
distance oxyanion2, /ela//A/7/o, /ela//B/195/n
distance oxyanion3, /ela//A/7/o, /ela//B/194/n

show nb_spher, wat1
show sticks, substrate
show sticks, 190s
show sticks, H57
show sticks, D102

# approximately the view in VVP4e, Fig.11-32 (p.348)
set_view (\
-0.732933760, 0.286370099, 0.617081881,\
0.456596434, 0.879488051, 0.134168610,\
-0.504288793, 0.380105615, -0.775372148,\
0.000203913, -0.000095243, -48.956962585,\
-8.940362930, 23.498645782, 37.284763336,\
40.323390961, 57.575588226, -20.000000000 )