Complex 5vp2
System information
| Experimental technique | X-ray |
| Experimental resolution | 2.80 |
| System mass | 4571.58 kDa |
| Deposition year | 2017 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Thermus |
| RCSB PDB Entry | 5vp2 |
| Reference | Osterman Ilya A., Khabibullina Nelli F., Komarova Ekaterina S., Kasatsky Pavel, Kartsev Victor G., Bogdanov Alexey A., Dontsova Olga A., Konevega Andrey L., Sergiev Petr V., Polikanov Yury S.. . Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state Nucleic Acids Research |
| Equivalence Class |
NR_all_97519.80
BGSU version: 4.48 |
| Compound | M2D |
| Residue | . / 4118 |
| Chain | HUA / 1A |
| Non-redundant | True |
| Interacting RNA chains | A/1A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | A/1A: rRNA |
| RNA family global | rRNA |
| Volume | 955.60 Å3 |
| Hydrophobicity | 0.441 |
| Hydrophilicity | 1.765 |
| Buriedness | 0.802 |
| Don/acc character | 0.534 |
| SiteScore | 1.220 |
| D Score | 0.846 |
| Kd | — |
| Compound | M2D |
| Residue | . / 3864 |
| Chain | XTC / 2A |
| Non-redundant | True |
| Interacting RNA chains | EB/2A |
| RNA environment detailled | ion |
| RNA environment global | RNA |
| RNA family chains | EB/2A: rRNA |
| RNA family global | rRNA |
| Volume | 654.79 Å3 |
| Hydrophobicity | 0.917 |
| Hydrophilicity | 1.209 |
| Buriedness | 0.807 |
| Don/acc character | 0.674 |
| SiteScore | 1.223 |
| D Score | 1.030 |
| Kd | — |