TABLE 2.
Description of the side chain pockets, including the amino acids lining the pockets, the number of ordered water molecules per pocket, and the overall hydrophobicity of pockets in PrgZ, OppA, AppA, and DppA
The numbering of the pockets is based on the cCF10 ligand in PrgZ; the numbering of the pockets of OppA and AppA is shown in parentheses. The hydrophobicity description is based on inspection of the side chain pockets in each of the proteins. “Mixed” means that both hydrophilic and hydrophobic residues line the pocket. A dash indicates that the side chain pocket does not exist in that protein. We also note that in OppA from L. lactis, most of the pockets are not well defined, and instead, a large cavity is present that even allows peptides to bind in different register (14, 32). The data were generated using the following Protein Data Bank codes: OppA, 3DRG; AppA, 1XOC; and DppA, 1DPP.
| Side chain pocket | Residues lining the pocket (PrgZ) | Ordered water molecules (PrgZ) | Hydrophobicity |
|||
|---|---|---|---|---|---|---|
| PrgZ | OppA | AppA | DppA | |||
| – | – | Hydrophilic (1) | Hydrophilic (1) | – | ||
| – | – | – | Hydrophilic (2) | Hydrophilic (2) | – | |
| – | – | – | Mixed (3) | Mixed (3) | – | |
| 1 | Gln-81, Ile-84, Gln-470 | 1 | Mixed | Mixed (4) | Hydrophilic (4) | Mixed |
| 2 | Val-79, Met-454, Met-489, His-491 | 3 | Hydrophobic | Hydrophobic (5) | Hydrophobic (5) | Hydrophobic |
| 3 | Asn-318, Met-320, Gly-468, Gln-470 | 3 | Hydrophilic | Mixed (6) | Mixed (6) | – |
| 4 | Phe-453, Met-454, Leu-457, Ser-467 | 1 | Hydrophobic | Mixed (7) | Mixed (7) | – |
| 5 | Gly-67, Thr-68, Ser-418, Glu-423 | 4 | Hydrophilic | Hydrophilic (8) | Mixed (8) | – |
| 6 | Met-320, Leu-356, Phe-422, Glu-423, Ala-426, Phe-531 | 2 | Hydrophobic | Hydrophobic (9) | Mixed (9) | – |
| 7 | Ile-280, Pro-296, Ala-298, Phe-422 | 3 | Hydrophobic | – | – | – |