MolNFT v1 · #46429 · RNA
Structure of the 23S rRNA of the large ribosomal subunit from deinococcus radiodurans in complex with the macrolide ru-69874
2O45: “Structure of the 23S rRNA of the large ribosomal subunit from deinococcus radiodurans in complex with the…”. X-ray diffraction, 1 ligand (RU6), 20 pockets (best druggability 0.85). MolNFT v1 #46429 on GenesisL1: 3D structure…
- PDB
- 2O45
- Type
- RNA
- Length
- 2,766 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S rRNA
- Ligands
- RU6
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S rRNA | rna | 2766 | — | — |
Ligands and binding sites
- RU6 · (3as,4r,7r,8s,9s,10r,11r,13r,15r,15ar)-4-ethyl-11-methoxy-3A,7,9,11,13,15-hexamethyl-2,6,14-trioxo-1-[4-(4-pyridin-3-yl-1H-imidazol-1-yl)butyl]-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside · ligand · chains A
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 | 1005 | 0.85 | 0.87 | 81 | empty |
| 2 | 988 | 0.85 | 0.87 | 81 | empty |
| 3 | 924 | 0.84 | 0.87 | 77 | empty |
| 4 | 865 | 0.82 | 0.85 | 58 | empty |
| 5 | 782 | 0.80 | 0.85 | 61 | empty |
Compared structures
- 2O45 · Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2O45 · PDBe 2O45
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