Complex 4v6m
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 | Electron Microscopy |
| Experimental resolution | 7.10 |
| System mass | 2410.93 kDa |
| Deposition year | 2011 |
| Molecule type | RNA/Protein |
| # RNA entities | 1 |
| Organism | Escherichia |
| RCSB PDB Entry | 4v6m |
| Reference | Frauenfeld Jens, Gumbart James, Sluis Eli O van der, Funes Soledad, Gartmann Marco, Beatrix Birgitta, Mielke Thorsten, Berninghausen Otto, Becker Thomas, Schulten Klaus, Beckmann Roland. 2011. Cryo-EM structure of the ribosome–SecYE complex in the membrane environment Nature Structural & Molecular Biology |
| Equivalence Class |
NR_all_83717.187
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 | PEV |
| Residue | . / 3001 |
| Chain | YD / B8 |
| Non-redundant | True |
| Interacting RNA chains | BA/B8 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | BA/B8: rRNA |
| RNA family global | rRNA |
| Volume | 593.39 Å3 |
| Hydrophobicity | 2.919 |
| Hydrophilicity | 0.280 |
| Buriedness | 0.792 |
| Don/acc character | 3.920 |
| SiteScore | 1.209 |
| D Score | 1.324 |
| Kd | — |
| Compound | PEV |
| Residue | . / 3004 |
| Chain | BE / B8 |
| Non-redundant | True |
| Interacting RNA chains | BA/B8 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | BA/B8: rRNA |
| RNA family global | rRNA |
| Volume | 672.28 Å3 |
| Hydrophobicity | 2.810 |
| Hydrophilicity | 0.431 |
| Buriedness | 0.858 |
| Don/acc character | 3.720 |
| SiteScore | 1.224 |
| D Score | 1.314 |
| Kd | — |
| Compound | PEV |
| Residue | . / 3006 |
| Chain | DE / B8 |
| Non-redundant | True |
| Interacting RNA chains | BA/B8 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | BA/B8: rRNA |
| RNA family global | rRNA |
| Volume | 482.60 Å3 |
| Hydrophobicity | 1.897 |
| Hydrophilicity | 0.507 |
| Buriedness | 0.806 |
| Don/acc character | 3.521 |
| SiteScore | 1.175 |
| D Score | 1.258 |
| Kd | — |
| Compound | PGV |
| Residue | . / 3005 |
| Chain | CE / B8 |
| Non-redundant | True |
| Interacting RNA chains | BA/B8 |
| RNA environment detailled | other |
| RNA environment global | RNA/Other |
| RNA family chains | BA/B8: rRNA |
| RNA family global | rRNA |
| Volume | 528.91 Å3 |
| Hydrophobicity | 2.079 |
| Hydrophilicity | 0.604 |
| Buriedness | 0.752 |
| Don/acc character | 1.736 |
| SiteScore | 1.120 |
| D Score | 1.194 |
| Kd | — |