Research workbench
Models for the T. thermophilus ribosome recycling factor bound to the E. COLI post-termination complex
Analyse Models for the T. thermophilus ribosome recycling factor bound to 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
- 3J0D
- Type
- protein + RNA
- Length
- 625 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal 23S RNA; 50S ribosomal protein L11; Ribosomal 16S RNA; 30S ribosomal protein…
- UniProt
- P0A7J7, P0A7S3, Q9WX76
- Pockets
- 7 · best druggability 0.75
Structure
electron microscopy · 11 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal 23S RNA | rna | 50 | — | — |
| B | Ribosomal 23S RNA | rna | 22 | — | — |
| C | Ribosomal 23S RNA | rna | 17 | — | — |
| D | Ribosomal 23S RNA | rna | 13 | — | — |
| E | Ribosomal 23S RNA | rna | 19 | — | — |
| F | Ribosomal 23S RNA | rna | 19 | — | — |
| G | 50S ribosomal protein L11 | protein | 141 | 38% helix, 18% strand | P0A7J7 |
| H | Ribosomal 16S RNA | rna | 18 | — | — |
| h | Ribosomal 16S RNA | rna | 19 | — | — |
| I | 30S ribosomal protein S12 | protein | 122 | 5% helix, 14% strand | P0A7S3 |
| J | Ribosome-recycling factor | protein | 185 | 62% helix, 14% strand | Q9WX76 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.75 | 0.78 | 77 | empty |
| 2 | 623 | 0.63 | 0.75 | 35 | empty |
| 3 | 233 | 0.62 | 0.82 | 29 | empty |
| 4 | 108 | 0.51 | 0.83 | 13 | empty |
| 5 | 107 | 0.40 | 0.77 | 14 | empty |
Interfaces
15 interfaces between chains.
- A–G · 1063 Ų buried · 27 hydrogen bonds · protein-nucleic
- H–h · 1025 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- H–I · 254 Ų buried · 14 hydrogen bonds · protein-nucleic
- h–I · 251 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–H · 180 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 3J0D · Models for the T. thermophilus ribosome recycling factor bound to the E. coli… · the same entry in another collection · chain J against J, TM-score 1.00
- Q9WX76 · AlphaFold monomer V2.0 prediction for ribosome-recycling factor (Q9WX76) · a predicted model of the same protein · chain J against A, TM-score 0.63
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 P0A7J7
- Every structure of UniProt P0A7S3
- Every structure of UniProt Q9WX76
- Elsewhere: RCSB PDB 3J0D · PDBe 3J0D · UniProt P0A7J7 · UniProt P0A7S3 · UniProt Q9WX76
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