Research workbench
Structure of ribosome binding domain of the trigger factor on the 50S ribosomal subunit from D. radiodurans
Analyse Structure of ribosome binding domain of the trigger factor on the 50S ribosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D3O
- Type
- protein + RNA
- Length
- 3,171 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L23; 50S ribosomal protein L24; 50S ribosomal…
- UniProt
- Q9RXK0, Q9RXJ1, Q9RXJ4, Q9RT21
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2802 | — | — |
| R | 50S ribosomal protein L23 | protein | 93 | 16% helix, 9% strand | Q9RXK0 |
| S | 50S ribosomal protein L24 | protein | 110 | 3% helix, 23% strand | Q9RXJ1 |
| W | 50S ribosomal protein L29 | protein | 66 | 50% helix, 0% strand | Q9RXJ4 |
| 1 | Trigger factor | protein | 100 | 38% helix, 14% strand | Q9RT21 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.86 | 0.90 | 83 | empty |
| 2 | 1012 | 0.86 | 0.88 | 96 | empty |
| 3 | 997 | 0.85 | 0.88 | 85 | empty |
| 4 | 862 | 0.83 | 0.86 | 61 | empty |
| 5 | 1171 | 0.82 | 0.84 | 83 | empty |
Interfaces
8 interfaces between chains.
- 0–R · 1834 Ų buried · 37 hydrogen bonds · protein-nucleic
- 0–S · 1819 Ų buried · 31 hydrogen bonds · protein-nucleic
- 0–W · 896 Ų buried · 17 hydrogen bonds · protein-nucleic
- R–1 · 395 Ų buried · 10 hydrogen bonds · protein-protein
- R–W · 376 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2D3O · Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit… · the same entry in another collection · chain 1 against 1, TM-score 1.00
- Q9RXJ4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L29 (Q9RXJ4) · a predicted model of the same protein · chain W against A, TM-score 0.82
- Q9RXK0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L23 (Q9RXK0) · a predicted model of the same protein · chain R against A, TM-score 0.81
- Q9RXJ1 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L24 (Q9RXJ1) · a predicted model of the same protein · chain S against A, TM-score 0.73
- Q9RT21 · AlphaFold monomer V2.0 prediction for trigger factor (Q9RT21) · a predicted model of the same protein · chain 1 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 Q9RXK0
- Every structure of UniProt Q9RXJ1
- Every structure of UniProt Q9RXJ4
- Every structure of UniProt Q9RT21
- Elsewhere: RCSB PDB 2D3O · PDBe 2D3O · UniProt Q9RXK0 · UniProt Q9RXJ1 · UniProt Q9RXJ4 · UniProt Q9RT21
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