Table 4. Polar contacts detected using the pentasaccharide–AT X-ray structure [6] and the octasaccaride B–AT (best scored docking output structures) complexes.
Interactions were assumed to occur between ligand–protein polar groups closer than 6 Å. Listed contacts refer to the best scored conformers predicted by AutoDock. The AGA*IA sequence is shown in bold.
| Octasaccharide B | ||||
|---|---|---|---|---|
| Residue | Polar group | AGA*IA X-ray structure [6] | IdoA 2S0 | IdoA 1C4 |
| ΔU2S | COO | Lys136† | ||
| GlcNNS,6S | NS | Arg132 | Arg132 | |
| Lys133 | ||||
| IdoA | ||||
| GlcNNS,6S | 6S | Lys125 | Lys125 | Lys125 |
| Arg129 | ||||
| Arg132 | Arg132 | |||
| GlcA | COO | Lys11 | Lys11 | Lys11 |
| Asn45 | Asn45 | Asn45 | ||
| Lys125 | Lys125 | Lys125 | ||
| GlcNNS,3,6S | NS | Arg13 | Arg13 | Arg13 |
| Lys114 | Lys114 | Lys114 | ||
| 3S | Lys114 | Lys114 | Lys114 | |
| IdoA2S* | COO | Arg47 | Arg47 | Arg47 |
| Lys114 | Lys114 | Lys114 | ||
| GlcNNS,6S | NS | Arg46 | Arg46 | Arg46 |
| Arg47 | Arg47 | Arg47 | ||
| 3S | Arg46 | |||
| Arg47 | ||||
†Weak interactions: distance ≈ 8 Å.