Interaction of the P3-P4′ residues at the R506 site of cleavage of FVa with APC. APC in the FVa-APC complex is rendered in cartoon representation (cyan) in the standard Bode orientation⁵³ (A) and compared with the PPACK-bound APC^28,29 (B). The difference in resolution between the 2 structures is only 0.3 Å. (A) The P3-P4′ residues of FVa are rendered as sticks (yellow) with the density shown as a mesh (green). The most striking difference between the 2 structures is the position of the autolysis loop that is critical for directing cleavage of FVa to R506 rather than R306.⁶⁸ The latch of FVa would come in direct collision with R312(c149d) in the autolysis loop of APC and forces a 26 Å relocation of the guanidinium group of this residue toward E357(c192) near the active site entrance. The shift shrinks the width of the autolysis loop measured as the Cα-Cα distance between S304(c145) and R312(c149d) from 19 Å to 6.2 Å. The conformational transition is further stabilized by interactions of R306(c147) with E357(c192) and Q509 (Table 2) at P3′, causing E357(c192) to point away from D504 at P3 and remove any potential electrostatic clash. Residue R506 binds to the S1 site by engaging D354(c189) in a bidentate H-bond. Additional contacts in the active site region involve D504 at P3, [polar with G381(c216), hydrophobic with G381(c216), and E382(c217)], R505 at P2 [hydrophobic with the catalytic H211(c57) and W380(c215)], I508 at P2′ [hydrophobic with A195(c41), Y302(c143), and G358(c193)], and R510 at P4′ [salt bridge and hydrophobic with E215(c60a)]. R507 at P1′ is exposed to solvent. (B) The PPACK (green sticks) inhibited structure of APC is similar overall to the FVa-bound structure of APC, as shown in panel A, except for the large conformation changes taking place in the autolysis loop. Residues in this panel are also labeled according to chymotrypsin to facilitate comparison.