Research workbench
Models for the T. thermophilus ribosome recycling factor and the E. COLI elongation factor G bound to the E. COLI post-termination complex
Analyse Models for the T. thermophilus ribosome recycling factor and the E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J0E
- Type
- protein + RNA
- Length
- 1,118 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal 23S RNA; Ribosomal 16S RNA; 30S ribosomal protein S12; Ribosome-recycling…
- UniProt
- P0A7S3, Q9WX76, P0A6M8
- Pockets
- 15 · best druggability 0.79
Structure
electron microscopy · 9 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal 23S RNA | rna | 22 | — | — |
| B | Ribosomal 23S RNA | rna | 17 | — | — |
| C | Ribosomal 23S RNA | rna | 13 | — | — |
| D | Ribosomal 23S RNA | rna | 19 | — | — |
| E | Ribosomal 16S RNA | rna | 18 | — | — |
| e | Ribosomal 16S RNA | rna | 19 | — | — |
| F | 30S ribosomal protein S12 | protein | 123 | 5% helix, 14% strand | P0A7S3 |
| G | Ribosome-recycling factor | protein | 185 | 59% helix, 14% strand | Q9WX76 |
| H | Elongation factor G | protein | 702 | 29% helix, 26% strand | P0A6M8 |
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.79 | 0.80 | 99 | empty |
| 2 | 102 | 0.78 | 0.98 | 21 | empty |
| 3 | 57 | 0.73 | 0.99 | 18 | empty |
| 4 | 769 | 0.71 | 0.77 | 56 | empty |
| 5 | 434 | 0.58 | 0.75 | 22 | empty |
Interfaces
15 interfaces between chains.
- G–H · 1724 Ų buried · 43 hydrogen bonds · protein-protein
- E–e · 1023 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–G · 198 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–e · 196 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- F–H · 189 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3J0E · Models for the T. thermophilus ribosome recycling factor and the E. coli elongation… · the same entry in another collection · chain H against H, TM-score 1.00
- P0A6M8 · AlphaFold monomer V2.0 prediction for elongation factor G (P0A6M8) · a predicted model of the same protein · chain H against A, TM-score 0.82
- Q9WX76 · AlphaFold monomer V2.0 prediction for ribosome-recycling factor (Q9WX76) · a predicted model of the same protein · chain G against A, TM-score 0.70
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 P0A7S3
- Every structure of UniProt Q9WX76
- Every structure of UniProt P0A6M8
- Elsewhere: RCSB PDB 3J0E · PDBe 3J0E · UniProt P0A7S3 · UniProt Q9WX76 · UniProt P0A6M8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.