Complex 5cd1
Legend
Pocket colors by molecule type
RNA
Protein
DNA
These colors appear when a pocket is selected (the structure fades to show the pocket surface). Colors from the molecule-type palette (RNA / protein / DNA).
System information
| Experimental technique | X-ray |
| Experimental resolution | 3.60 |
| System mass | 225.01 kDa |
| Deposition year | 2015 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Homo |
| RCSB PDB Entry | 5cd1 |
| Reference | Finer-Moore Janet, Czudnochowski Nadine, O'Connell Joseph D., Wang Amy Liya, Stroud Robert M.. 2015. Crystal Structure of the Human tRNA m1A58 Methyltransferase–tRNA3Lys Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target Journal of Molecular Biology |
| Equivalence Class |
NR_all_72172.3
BGSU version: 4.52 |
Pockets List
Legend
Cell colors for SiteScore and D Score:
Favourable
Intermediate
Unfavourable
Not available
| Score | Threshold | Meaning |
|---|---|---|
| SiteScore | < 0.8 | Non-drug binding site |
| SiteScore | 0.8 – 1.0 | Potential drug binding site |
| SiteScore | > 1.0 | Promising binding site |
| D Score | < 0.83 | Undruggable |
| D Score | 0.83 – 0.98 | Difficult |
| D Score | > 0.98 | Druggable |
Tick a pocket below to highlight it in the 3D structure above.
| Compound | SAH |
| Residue | . / 301 |
| Chain | G / A |
| Non-redundant | True |
| Interacting RNA chains | E/M |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | E/M: tRNA |
| RNA family global | tRNA |
| Volume | 325.16 Å3 |
| Hydrophobicity | 1.080 |
| Hydrophilicity | 1.176 |
| Buriedness | 0.867 |
| Don/acc character | 0.925 |
| SiteScore | 1.113 |
| D Score | 1.077 |
| Kd | — |
| Compound | SAH |
| Residue | . / 301 |
| Chain | H / D |
| Non-redundant | True |
| Interacting RNA chains | F/N |
| RNA environment detailled | protein |
| RNA environment global | RNA/Protein |
| RNA family chains | F/N: tRNA |
| RNA family global | tRNA |
| Volume | 248.68 Å3 |
| Hydrophobicity | 0.867 |
| Hydrophilicity | 1.155 |
| Buriedness | 0.844 |
| Don/acc character | 0.656 |
| SiteScore | 1.097 |
| D Score | 1.070 |
| Kd | — |