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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.