Research workbench
The crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (sb-275833)
Analyse The crystal structure of the 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
- 2OGO
- Type
- protein + RNA
- Length
- 2,970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 50S ribosomal protein L3
- UniProt
- Q9RXK2
- Ligands
- G34
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2765 | — | — |
| B | 50S ribosomal protein L3 | protein | 205 | 0% helix, 0% strand | Q9RXK2 |
Ligands and binding sites
- G34 · Retapamulin · ligand · chains 0
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 | 963 | 0.85 | 0.88 | 75 | empty |
| 2 | 955 | 0.85 | 0.87 | 81 | empty |
| 3 | 684 | 0.83 | 0.88 | 59 | empty |
| 4 | 658 | 0.82 | 0.87 | 79 | empty |
| 5 | 476 | 0.80 | 0.88 | 44 | empty |
Interfaces
1 interface between chains.
- 0–B · 2064 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2OGO · The crystal structure of the large ribosomal subunit from Deinococcus radiodurans… · the same entry in another collection · chain 0 against 0, TM-score 1.00
- Q9RXK2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L3 (Q9RXK2) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q9RXK2
- Elsewhere: RCSB PDB 2OGO · PDBe 2OGO · UniProt Q9RXK2
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