Research workbench
The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with troleandomycin macrolide antibiotic
Analyse The crystal structure of the 50S large ribosomal subunit from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OND
- Type
- protein + RNA
- Length
- 2,953 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L22; 50S ribosomal protein L32
- UniProt
- Q9RXJ7, P49228
- Ligands
- TAO
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2765 | — | — |
| Q | 50S ribosomal protein L22 | protein | 130 | 0% helix, 0% strand | Q9RXJ7 |
| Z | 50S ribosomal protein L32 | protein | 58 | 0% helix, 0% strand | P49228 |
Ligands and binding sites
- TAO · Troleandomycin · ligand · chains 0, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 812 | 0.86 | 0.90 | 72 | empty |
| 2 | 978 | 0.86 | 0.88 | 81 | empty |
| 3 | 1100 | 0.85 | 0.87 | 95 | empty |
| 4 | 608 | 0.84 | 0.90 | 56 | empty |
| 5 | 671 | 0.84 | 0.89 | 66 | empty |
Interfaces
3 interfaces between chains.
- 0–Z · 972 Ų buried · 0 hydrogen bonds · protein-nucleic
- 0–Q · 879 Ų buried · 0 hydrogen bonds · protein-nucleic
- Q–Z · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OND · The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans… · the same entry in another collection · chain 0 against 0, TM-score 1.00
- Q9RXJ7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L22 (Q9RXJ7) · a predicted model of the same protein · chain Q against A, TM-score 0.92
- P49228 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L32 (P49228) · a predicted model of the same protein · chain Z against A, TM-score 0.83
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 Q9RXJ7
- Every structure of UniProt P49228
- Elsewhere: RCSB PDB 1OND · PDBe 1OND · UniProt Q9RXJ7 · UniProt P49228
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