MolNFT v1 · #34054 · protein + RNA
Structure of ribosome binding domain of the trigger factor on the 50S ribosomal subunit from D. radiodurans
2D3O · 23S ribosomal RNA: “Structure of ribosome binding domain of the trigger factor on the 50S ribosomal subunit from D. radiodurans”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #34054 on GenesisL1: 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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