Table 2.
Similarity between R. palustris SBPs and their structural relatives
| RPA0668 PHB |
RPA0985 PHB |
RPB2270 PHB |
RPD1586 PHB |
RPD1586 DHB |
RPD1586 VLA |
PDB 3i45 |
PDB 3td9 |
PDB 3sg0 |
OX2-CX- C1-C6 torsion angle |
Cavity volume |
|
|---|---|---|---|---|---|---|---|---|---|---|---|
| RPA0668/BEZ | 0.43 (356) | 1.89 (341) | 1.88 (340) | 1.67 (346) | 1.67 (346) | 1.66 (344) | 2.20 (335) | 1.97 (336) | 2.18 (321) | −27.7 | 138.8 |
| RPA0668/PHB | — | 2.11 (340) | 1.89 (344) | 1.66 (342) | 1.65 (342) | 1.67 (342) | 2.27 (334) | 2.00 (329) | 2.14 (323) | −25.3 | 141.8 |
| RPA0985/PHB | 27.8/42.6 | — | 0.35 (368) | 1.47 (353) | 1.58 (355) | 1.56 (355) | 2.28 (343) | 2.07 (333) | 1.93 (314) | −20.9 | 154.1 |
| RPB2270/PHB | 27.7/43.1 | 90.0/94.1 | — | 1.47 (355) | 1.54 (354) | 1.52 (355) | 2.19 (342) | 2.15 (334) | 1.89 (322) | −24.2 | 153.6 |
| RPD1586/PHB | 32.2/49.6 | 43.3/61.7 | 43.8/62.7 | — | 0.17 (363) | 0.15 (363) | 2.32 (344) | 2.33 (336) | 2.19 (323) | −33.7 | 179.7 |
| RPD1586/DHB | 32.2/49.6 | 43.3/61.7 | 43.8/62.7 | 100 | — | 0.17 (363) | 2.34 (344) | 2.35 (337) | 2.09 (315) | −25.7 | 165.4 |
| RPD1586/VLA | 32.2/49.6 | 43.3/61.7 | 43.8/62.7 | 100 | 100 | — | 2.33 (346) | 2.33 (335) | 2.20 (323) | −27.4 | 175.1 |
| PDB 3i45 | 22.7/38.0 | 22.2/37.8 | 22.6/37.3 | 24.5/42.4 | 24.5/42.4 | 24.5/42.4 | 128.0 | ||||
| PDB 3td9 | 20.5/33.6 | 24.3/35.5 | 25.8/40.5 | 24.9/45.3 | 24.9/45.3 | 24.9/45.3 | 235.0 | ||||
| PDB 3sg0 | 23.1/36.3 | 23.5/40.4 | 23.4/39.6 | 24.8/42.0 | 24.8/42.0 | 24.8/42.0 | 228.9 |
The molecules were superposed in Coot.46 If multiple protein chains exist in the asymmetric unit, only chain A was compared. Sequence identity was determined using the EMBOSS Needle program.47 Cavity volumes were calculated in SUFRNET with 1.2Å radius for gap spheres.48 For calculations, double conformations were removed and conformer A was used. Hydrogen atoms were not included. Selenium atoms were treated as sulfur atoms. The volumes refer to molecules listed in the first column. The upper right side of the table shows rmsd (in angstroms) with number of superimposed Cα atoms (in parentheses); the lower left side of the table shows sequence identity and similarity (in percentage). The torsion angles defining conformation of BEZ derivatives are provided (in degrees, chain A ligand). The far right column shows cavity volume (in cubic angstroms).