Complex 4wt8
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 | 3.40 |
| System mass | 4460.70 kDa |
| Deposition year | 2014 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 4wt8 |
| Reference | Amunts Alexey, Fiedorczuk Karol, Truong Thao T., Chandler Josephine, Greenberg E. Peter, Ramakrishnan V.. 2015. Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics Journal of Molecular Biology |
| Equivalence Class |
NR_all_65795.87,
NR_all_97519.80,
NR_all_20721.12,
NR_all_47349.1
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 | 3V6 |
| Residue | . / 3001 |
| Chain | PD / C1 |
| Non-redundant | True |
| Interacting RNA chains | UA/C4, AC/C1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | AC/C1: rRNA, UA/C4: tRNA |
| RNA family global | multiple |
| Volume | 751.86 Å3 |
| Hydrophobicity | 0.318 |
| Hydrophilicity | 1.071 |
| Buriedness | 0.692 |
| Don/acc character | 2.430 |
| SiteScore | 1.146 |
| D Score | 1.006 |
| Kd | — |
| Compound | 3V6 |
| Residue | . / 3001 |
| Chain | RD / D1 |
| Non-redundant | True |
| Interacting RNA chains | EC/D4, LD/D1 |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EC/D4: tRNA, LD/D1: rRNA |
| RNA family global | multiple |
| Volume | 752.89 Å3 |
| Hydrophobicity | 0.250 |
| Hydrophilicity | 1.042 |
| Buriedness | 0.680 |
| Don/acc character | 2.157 |
| SiteScore | 1.138 |
| D Score | 1.008 |
| Kd | — |
| Compound | PAR |
| Residue | . / 1601 |
| Chain | ND / Ab |
| Non-redundant | True |
| Interacting RNA chains | V/Ab |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | V/Ab: rRNA |
| RNA family global | rRNA |
| Volume | 27.10 Å3 |
| Hydrophobicity | 0.301 |
| Hydrophilicity | 0.788 |
| Buriedness | 0.556 |
| Don/acc character | 2.488 |
| SiteScore | 0.624 |
| D Score | 0.402 |
| Kd | — |
| Compound | PAR |
| Residue | . / 1601 |
| Chain | OD / Bb |
| Non-redundant | True |
| Interacting RNA chains | X/Bb |
| RNA environment detailled | RNA-only |
| RNA environment global | RNA |
| RNA family chains | X/Bb: rRNA |
| RNA family global | rRNA |
| Volume | 26.75 Å3 |
| Hydrophobicity | 0.302 |
| Hydrophilicity | 0.738 |
| Buriedness | 0.555 |
| Don/acc character | 3.692 |
| SiteScore | 0.633 |
| D Score | 0.418 |
| Kd | — |