Research workbench
Etta binds to ribosome exit site and regulates translation by restricting ribosome and tRNA dynamics
Analyse Etta binds to ribosome exit site and regulates translation by restricting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J5S
- Type
- protein + RNA
- Length
- 1,450 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; 23S ribosomal RNA; P-site tRNA fmet; Energy-dependent translational…
- UniProt
- P0A9W3, P0A7L0, P62399, P0A7N9, P02359
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 16S ribosomal RNA | rna | 32 | — | — |
| A | 23S ribosomal RNA | rna | 174 | — | — |
| E | P-site tRNA fmet | rna | 77 | — | — |
| D | Energy-dependent translational throttle a (etta) | protein | 554 | 41% helix, 23% strand | P0A9W3 |
| F | 50S ribosomal protein L1 | protein | 234 | 27% helix, 19% strand | P0A7L0 |
| G | 50S ribosomal protein L5 | protein | 178 | 35% helix, 18% strand | P62399 |
| H | 50S ribosomal protein L33 | protein | 50 | 0% helix, 42% strand | P0A7N9 |
| I | 30S ribosomal protein S7 | protein | 151 | 58% helix, 8% strand | P02359 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.82 | 0.84 | 76 | empty |
| 2 | 1083 | 0.81 | 0.83 | 68 | empty |
| 3 | 577 | 0.78 | 0.84 | 86 | empty |
| 4 | 330 | 0.72 | 0.85 | 35 | empty |
| 5 | 668 | 0.70 | 0.78 | 49 | empty |
Interfaces
11 interfaces between chains.
- A–F · 2969 Ų buried · 78 hydrogen bonds · protein-nucleic
- A–D · 1311 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–F · 1141 Ų buried · 20 hydrogen bonds · protein-protein
- D–I · 742 Ų buried · 20 hydrogen bonds · protein-protein
- E–D · 487 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3J5S · EttA binds to ribosome exit site and regulates translation by restricting ribosome and… · the same entry in another collection · chain I against I, TM-score 1.00
- P0A7L0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P0A7L0) · a predicted model of the same protein · chain F against A, TM-score 0.74
- P0A9W3 · AlphaFold monomer V2.0 prediction for energy-dependent translational throttle protein… · a predicted model of the same protein · chain D against A, TM-score 0.68
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A9W3
- Every structure of UniProt P0A7L0
- Every structure of UniProt P62399
- Every structure of UniProt P0A7N9
- Every structure of UniProt P02359
- Elsewhere: RCSB PDB 3J5S · PDBe 3J5S · UniProt P0A9W3 · UniProt P0A7L0 · UniProt P62399 · UniProt P0A7N9 · UniProt P02359
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