Complex 7md7
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.80 |
| System mass | 4428.45 kDa |
| Deposition year | 2021 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 7md7 |
| Reference | Chen Chih-Wei, Pavlova Julia A., Lukianov Dmitrii A., Tereshchenkov Andrey G., Makarov Gennady I., Khairullina Zimfira Z., Tashlitsky Vadim N., Paleskava Alena, Konevega Andrey L., Bogdanov Alexey A., Osterman Ilya A., Sumbatyan Natalia V., Polikanov Yury S.. . Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome Antibiotics |
| Equivalence Class |
NR_all_97519.80,
NR_all_42622.80
BGSU version: 4.49 |
| Compound | ARG |
| Residue | . / 228 |
| Chain | TSA / 1B |
| Non-redundant | True |
| Interacting RNA chains | B/1B |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | B/1B: rRNA |
| RNA family global | rRNA |
| Volume | 98.44 Å3 |
| Hydrophobicity | 0.054 |
| Hydrophilicity | 1.775 |
| Buriedness | 0.575 |
| Don/acc character | 0.983 |
| SiteScore | 0.868 |
| D Score | 0.450 |
| Kd | — |
| Compound | ARG |
| Residue | . / 316 |
| Chain | GUA / 1F |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | - |
| Hydrophobicity | - |
| Hydrophilicity | - |
| Buriedness | - |
| Don/acc character | - |
| SiteScore | - |
| D Score | - |
| Kd | — |
| Compound | YXM |
| Residue | . / 4055 |
| Chain | QRA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 529.94 Å3 |
| Hydrophobicity | 0.540 |
| Hydrophilicity | 1.686 |
| Buriedness | 0.781 |
| Don/acc character | 0.540 |
| SiteScore | 1.206 |
| D Score | 0.859 |
| Kd | — |
| Compound | YXM |
| Residue | . / 3758 |
| Chain | ZMC / 2A |
| Non-redundant | True |
| Interacting RNA chains | BB/2A |
| RNA environment detailled | protein, ion |
| RNA environment global | RNA/Protein |
| RNA family chains | BB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 570.41 Å3 |
| Hydrophobicity | 0.835 |
| Hydrophilicity | 1.097 |
| Buriedness | 0.775 |
| Don/acc character | 0.833 |
| SiteScore | 1.202 |
| D Score | 1.047 |
| Kd | — |