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Table 2 Clustering of the sampled phase space

From: A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail

Protein subunit

C α -backbone RMSD (Å)

Active site RMSD (Å)

% representation

Cluster 1B#,*

0.00

0.00

67.74

Cluster 2B*

1.46

1.86

19.20

Cluster 3B*

1.19

1.32

6.62

Cluster 4B

1.45

1.89

0.24

Cluster 5B*

0.72

0.69

0.22

Cluster 1C*

1.67

2.25

34.24

Cluster 2C

1.56

1.99

26.32

Cluster 3C

1.59

2.00

19.32

Cluster 4C

1.38

1.74

6.69

Cluster 5C*

1.80

2.40

6.74

PDB:2PT9A

1.56

1.99

-

PDB:2PT9B

1.65

2.17

-

PDB:2PT9C

3.77

3.68

-

  1. #Reference structure.
  2. *Structures selected to represent the sub-ensemble.
  3. The protein subunits represent the top five clusters of subunits B and C from MD. The representation of the sampled space of each cluster from the MD is given as a percentile of the total sampled space per subunit. The subunits of the ligand bound crystal structure [PDB:2PT9] with its Cα-backbone and active site RMSD values are included.
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Malaria Journal

ISSN: 1475-2875

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