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Figure 3.
Figure 3. Superposition of the S1 pockets of GPLGS-WT and WT
SARS-CoV M^pro (in stereo). (a) Superposition of the S1 pockets
in protomer A of GPLGS-WT and that of protomer A* of WT SARS-CoV
M^pro. Protomer A* of WT is in blue; protomer A of GPLGS-WT is
in yellow; protomer B* of WT is in magenta; protomer B of
GPLGS-WT is in red. In the WT structure, the amino group (NH[2])
of Ser1 in protomer B* donates a 3.0 Å hydrogen bond to
the carboxylate group of Glu166 and a 2.7 Å hydrogen bond
to the main-chain carbonyl group of Phe140 in protomer A*,
stabilizing the S1 pocket. The NH of Gly143 moves 0.8 Å
toward the activity site; the main chain of residues 142-143
moves toward the S1 subsite; the side-chain of Asn-A*142 flips
over with a 6 Å shift compared with protomer A of
GPLGS-WT. (b) Superposition of the S1 pockets in protomer B of
GPLGS-WT and that of Protomer A* of WT SARS-CoV M^pro. Protomer
A* of WT is in blue; protomer B of GPLGS-WT is in yellow;
protomer B* of WT is in magenta; protomer A of GPLGS-WT is in
red. The S1 pocket of protomer B collapses partly with
reorientation of Glu166 and residues 140–143. No electron
density was visible for residues A1 and A2. Figure 3.
Superposition of the S1 pockets of GPLGS-WT and WT SARS-CoV
M^pro (in stereo). (a) Superposition of the S1 pockets in
protomer A of GPLGS-WT and that of protomer A* of WT SARS-CoV
M^pro. Protomer A* of WT is in blue; protomer A of GPLGS-WT is
in yellow; protomer B* of WT is in magenta; protomer B of
GPLGS-WT is in red. In the WT structure, the amino group (NH[2])
of Ser1 in protomer B* donates a 3.0 Å hydrogen bond to
the carboxylate group of Glu166 and a 2.7 Å hydrogen bond
to the main-chain carbonyl group of Phe140 in protomer A*,
stabilizing the S1 pocket. The NH of Gly143 moves 0.8 Å
toward the activity site; the main chain of residues 142-143
moves toward the S1 subsite; the side-chain of Asn-A*142 flips
over with a 6 Å shift compared with protomer A of
GPLGS-WT. (b) Superposition of the S1 pockets in protomer B of
GPLGS-WT and that of Protomer A* of WT SARS-CoV M^pro. Protomer
A* of WT is in blue; protomer B of GPLGS-WT is in yellow;
protomer B* of WT is in magenta; protomer A of GPLGS-WT is in
red. The S1 pocket of protomer B collapses partly with
reorientation of Glu166 and residues 140–143. No electron
density was visible for residues A1 and A2.
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