Table 2.

Main molecular contacts <5 Å among the components of the prothrombin-fVa-fXa complex

fVa-fXaProthrombin-fXaProthrombin-fVa
A511-L352(c170) K307-Q240(c61) L260-T305* 
A511-I357(c175) D318-R405(c222) D261-K309* 
F576-R347(c165) D318-K408(c224) D265-K309* 
D577-R347(c165) R320-E372(c188) R266-A694* 
T579-K351(c169) E323-K330(c148) E269-R505 
T626-N348(c166) D326-K242(c62) R271-D697* 
D628-R347(c165)  R310-Y698 
E662-R306(c125)*  L312-Y698 
E662-K420(c236)*  L313-L702* 
E669-R306(c125)  P534-Y696* 
E672-R306(c125)*  F535-Y696* 
E672-Q360(c178)*   
E672-K414(c230)*   
V675-R424(c240)*   
E686-K276(c96)   
S1598-E82   
T1679-F84   
H1683-L91   
Y2021-E39*   
fVa-fXaProthrombin-fXaProthrombin-fVa
A511-L352(c170) K307-Q240(c61) L260-T305* 
A511-I357(c175) D318-R405(c222) D261-K309* 
F576-R347(c165) D318-K408(c224) D265-K309* 
D577-R347(c165) R320-E372(c188) R266-A694* 
T579-K351(c169) E323-K330(c148) E269-R505 
T626-N348(c166) D326-K242(c62) R271-D697* 
D628-R347(c165)  R310-Y698 
E662-R306(c125)*  L312-Y698 
E662-K420(c236)*  L313-L702* 
E669-R306(c125)  P534-Y696* 
E672-R306(c125)*  F535-Y696* 
E672-Q360(c178)*   
E672-K414(c230)*   
V675-R424(c240)*   
E686-K276(c96)   
S1598-E82   
T1679-F84   
H1683-L91   
Y2021-E39*   

Residues are numbered sequentially and for fXa also according to chymotrypsin by parentheses.

*

Residues of fVa not previously listed as potential epitopes of recognition of prothrombin or fXa by a recent review of biochemical data and computational models.66 The review lists a total of 56 residues of the A2 domain and 35 residues of the A3 domain of fVa involved in the interaction with fXa. The cryo-EM structure documents only 11 residues in the A2 domain (A511, F576, D577, T579, T626, D628, E662, E669, E672, V675, E686), 3 of which not reported previously (E662, E672, V675), 3 in the A3 domain (S1598, T1679, H1683) and 1 in the C1 domain (Y2021) also not reported previously. The main interactions are shown in Figure 4B-C. The review also lists 23 residues in the A2 domain, 18 in the A3 domain and 10 in the C1 domain as interacting with prothrombin.66 The cryo-EM structure documents 2 residues in the A1 domain (T305, K309) not reported previously, 6 residues in the A2 domain (R505, A694, Y696, D697, Y698, L702), 4 of which (A694, Y696, D697, L702) not reported previously, and no contacts involving the A3 and C1 domains.

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