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Table 1 Internal pockets volume variations

From: Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

MD code Central cavity Primary funnel(chain A) Primary funnel(chain B) Secondary channel(chain A) Secondary channel(chain B)
B 375-250 < 400-350 475-500 250 = 325-125 <
C1 375-500 > 400-530 > 450 = 300 = 400-150 <
C2 375 = 350-400 475 = 250-300 300-400 >
D 425-350 < 350-400 375-300 < 200-350 > 400 =
E1 475-400 < 400-325 < 500-675 > 300 = 400-275 <
E2a 375-400 400-525 > 500-300 < 300 = 400 =
E2b 300-400 > 400-450 450-500 250-300 275-375 >
F 400 = 425-300 < 450-525 > 200-150 275-300
  1. Summary of the volume profiles (in Å3) over the time for central cavity, primary funnels and secondary channels of chain A and B for each simulation B-F tracked with fpocket2. The trend progression of the volume is summarized as follows: decrease (<), modest decrease (≤), constant (=), modest increase (≥), increase (>). The time-dependent volume-profiles are added in supplementary information as Figure. SI10.
  2. MD codes: B – PqsD apoform, C1 – PqsD-ACoA in chain B, C2 – PqsD with ACoA in the primary funnel of chain A and B, D – PqsD with Cys112-bound anthranilate (PqsD-CSJ), E1 - PqsD-CSJ with βK in the primary funnel of chain B, E2a - PqsD-CSJ with βK in the secondary channel of chain A, E2b - PqsD-CSJ with βK in the secondary funnel of chain A and B, F – PqsD with HHQ in the primary funnel of chain B.