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Table 1 Structural statistics of the APETx1 structures in the present study (recombinant protein; 20 conformers) and previous study (natural product; 25 conformers) [27]

From: Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization

 

Natural product [27]

Recombinant protein

PDB code

1WQK

7BWI

Experimental conditions

pH 3.0 and 280 K

pH 6.0 and 298 K

Distance restraints

Total NOE-derived restraints

751

766

Intraresidue restraints (|i-j| = 0)

366

131

Sequential restraints (|i-j| = 1)

140

216

Short-range restraints (2 ≤ |i-j| ≤ 4)

61

94

Long-range restraints (|i-j| ≥ 5)

184

325

Disulfide bond restraints

9

12

Dihedral angle restraints

20

41

Hydrogen-bond restraints

36

–

Root-mean-square deviation (RMSD) from mean coordinate structure (Ã…)a

Backbone heavy atoms

  

Residues 1–42

0.82 ± 0.17

0.66 ± 0.21

Residues 2–41

0.63 ± 0.13

0.48 ± 0.12

All heavy atoms

  

Residues 1–42

1.28 ± 0.17

1.01 ± 0.15

Residues 2–41

1.13 ± 0.15

0.95 ± 0.14

Analysis of the Ramachandran plot (%)b

Residues in favored regions

84.3

93.7

Residues in allowed regions

14.0

5.6

Ramachandran outliers

1.7

0.6

  1. aRoot-mean-square deviation (RMSD) is calculated by MOLMOL [30]. bStereochemical quality is evaluated according to MolProbity (http://molprobity.biochem.duke.edu/)