MolNFT v1 · #17249 · protein + RNA
The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with troleandomycin macrolide antibiotic
1OND · 23S ribosomal RNA: “The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with…”. X-ray diffraction, 1 ligand (TAO), 20 pockets (best druggability 0.86). MolNFT v1 #17249 on GenesisL1: 3D…
- 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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