Molecular Characterization and In Silico Analysis of Naturally Occurring TEM Beta-Lactamase Variants among Pathogenic Enterobacteriaceae Infecting Indian Patients
Table 2
Model validation of bla TEM variants and docking details of these variants with 3rd generation cephalosporins.
TEM variants
PDB ID of the templates (% sequence identity)
SAVES & ProSA result of protein validation
CASTp result of pockets (solvent accessible)
Antibiotics
Distance
Docking Energy (Kcal/mol)
Inhibition constant Ki (mM)
H-bonding residues
Residues involved in making hydrophobic contacts
-scores, ERRAT, and Verify3D
PROCHECK
Volume
Area
Area of pocket
TEM-1
1ZG4 (94%)
-scores: −7.46 ERRAT: 80.292 Verify3D: 80%
% % %
50.8
64.6
28.4
CAZ
2.6
−4.69
0.36
S70, S130, K234, A237, R244, and R275
Y105, N170, V216, E222, S235, G238, and M272
CTX
2.5
−4.59
0.43
E94, S130, A237, and R244
S70, Y105, N170, and G236
CEP
9.1
−3.98
1.21
Y105, E110, N132, and R244
S70, A237
TEM-116
1AXB (94%)
-scores: −6.93 ERRAT: 94.553 Verify3D: 80%
% % %
70.4
93.1
36.3
CAZ
17.5
−4.30
0.70
R95, S99
A188, K190
CTX
2.7
−5.37
0.12
S70, S130, S235, A237, and R244
Y105, N170, G236, and E240
CEP
8.1
−3.45
2.96
S70, N132
E104, Y105, P107, S130, P167, N170, S235, G236, and A237
TEM-1ike
1ZG4 (94%)
-scores: −6.93 ERRAT: 94.553 Verify3D: 80%
% % % %
27.5
44.0
24.5
CAZ
8.4
−4.29
0.72
V216, S235, and R244
Y105, S130, K215, and A237
CTX
2.5
−4.57
0.44
E104, R244, S235, S70, and A237
Y105, V216, G236, G238, E240, and M272
CEP
6.8
−3.13
5.10
S70, Y107, S130, S235, A237, and R244
V216, G236, and A270
TEM-169
1ZG4 (94%)
-scores: −6.93 ERRAT: 94.553 Verify3D: 80%
%
% %
19.3
31.1
18.5
CAZ
9.7
−4.60
0.42
S70, S130, K234, and S235
E104, Y105, N132, P167, N170, V216, A237, and E240
