MolNFT v1 · #46841 · protein + RNA
The crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with the pleuromutilin derivative sb-571519
2OGM · 23S ribosomal RNA: “The crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with the…”. X-ray diffraction, 1 ligand (G19), 20 pockets (best druggability 0.86). MolNFT v1 #46841 on GenesisL1: 3D…
- PDB
- 2OGM
- Type
- protein + RNA
- Length
- 2,971 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
- G19
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2766 | — | — |
| B | 50S ribosomal protein L3 | protein | 205 | 0% helix, 0% strand | Q9RXK2 |
Ligands and binding sites
- G19 · (2s,3ar,4r,5s,6s,8r,9r,9ar,10r)-2,5-dihydroxy-4,6,9,10-tetramethyl-1-oxo-6-vinyldecahydro-3A,9-prop[1]enocyclopenta[8]annulen-8-yl [(6-aminopyridazin-3-yl)carbonyl]carbamate · 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 | 1082 | 0.86 | 0.88 | 86 | empty |
| 2 | 880 | 0.85 | 0.88 | 70 | empty |
| 3 | 1039 | 0.85 | 0.87 | 91 | empty |
| 4 | 774 | 0.82 | 0.86 | 61 | empty |
| 5 | 459 | 0.78 | 0.88 | 40 | empty |
Interfaces
1 interface between chains.
- 0–B · 2153 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 2OGM · 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 2OGM · PDBe 2OGM · UniProt Q9RXK2
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