1gdt and 1rep are protein structures that have DNA bound - hence they have entries in the NDB. Both have a B-form double helix and the DNA in 1gdt has an overhanging base (i.e. it has one unpaired base at one end of the double helix).
HTH Motif Predictions
In the table below are the 4 protein structures you have made predictions on, identified by their PDB codes. Use the links in the predictions column to access the predictions for HTH motifs within each structure. A short description of the matches are given below the table.
| # | PDB code | Chain ID | File type | Predictions | 1 | 1gdt | A | Protein-DNA complex | link |
| 2 | 1rep | none | Protein-DNA complex | link |
| 3 | 3daa | A | Protein | link |
| 4 | 1hw5 | A | Protein | link |
1gdt is a known HTH DNA-binding protein: gamma-delta resolvase. This protein has a HTH motif spanning residues 161-181 (chain A).Both methods correctly predicted the motif. | 
|
1rep is a known HTH DNA-binding protein: replication initiator protein REPE54. This protein has a HTH motif that spans residues 64-87.However the HTH has an extended loop between H1 and H2 and this makes the predictions for this structure more difficult. The PDNA-pred tool does predict the motif but only as a border-line hit and with a confidence index of zero (i.e. no confidence that this is correct). The predictdnahth tool does not predict the motif at all. This example gives a good indication of the limitations of both methods and highlights the point that prediction methods are never 100% correct. | 
|
3daa is a aminotransferase enzyme with no known DNA binding HTH motifs.Both methods correctly predicted no motif present. | 
|
1hw5 is the catabolite gene activator protein that has a known DNA binding HTH motif that spans residues 168-192 (chain A).Both methods correctly predicted the motif. | 
|