MolNFT v1 · #68063 · protein + RNA
Etta binds to ribosome exit site and regulates translation by restricting ribosome and tRNA dynamics
3J5S · 16S ribosomal RNA: “Etta binds to ribosome exit site and regulates translation by restricting ribosome and tRNA dynamics”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #68063 on GenesisL1: 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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