# zymogen_overlay PyMOL script
# Chymotrypsin and chymotrypsinogen
# jdc 2014_11_04

# Article title: Is gamma-chymotrypsin a tetrapeptide acyl-enzyme
# adduct of gamma-chymotrypsin?
# chain D, the PGAY tetrapeptide adduct, is at occupancy 0.92
# covalently linked to Ser195 (chain C)

load 1gct.pdb, chy
# chain A residues 1-11, B = 16-146, C = 151-245
# chain D is a 4-residue fragment (500* -504)
select A, chain A
select B, chain B
select C, chain C
select D, chain D
select Ser195, resi 195
select His57, resi 57
select Asp102, resi 102
select oxyhole, resi 193-195
#select wat, resi 619
disable Asp102
center His57

# add hydrogen bonds between selections
h_add His57
select SD, Ser195 | Asp102
select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))
dist HBA, (His57 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, /chy/1GCT/B/57/ND1, /chy/1GCT/B/102/OD1

hide labels,HBA
hide labels,HBD

# chymotrypsinogen at 1.8 A resolution
# 2 molecules (A and B) in the asymmetric unit
load 2cga.pdb, zymo
select zymoA, zymo and chain A
select zymoB, zymo and chain B
select z-Ser195, resi 195 and zymo and chain A
select z-His57, resi 57 and zymo and chain A
select z-Asp102, resi 102 and zymo and chain A
select z-oxyhole, resi 193-195 and zymo and chain A
select z-waters, resn HOH and zymo and chain A
disable z-waters

align chy, zymoA

hide everything
color red, zymoA
show ribbon, zymoA
color blue, chy
show ribbon, chy

set sphere_scale=0.33
# show locations of c-alpha atoms for Ile16 and Asp189
# for both mature chymotrypsin and trypsinogen
show sphere, chy and id 72
show sphere, zymo and id 105
show sphere, chy and id 1335
show sphere, zymo and id 1395

References

  1. Dixon MM, Matthews BW. (1989) Is gamma-chymotrypsin a tetrapeptide acyl-enzyme adduct of alpha-chymotrypsin? Biochemistry 28: 7033-7038.
  2. Wang D, Bode W, Huber R. (1985) Bovine chymotrypsinogen A. X-ray crystal structure analysis and refinement of a new crystal form at 1.8 Å resolution. J. Mol. Biol. 185: 595-624.