Research workbench
The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with the antibiotic sparsomycin
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
- 1NJN
- Type
- RNA
- Length
- 2,766 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA
- Ligands
- SPS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2766 | — | — |
Ligands and binding sites
- SPS · Sparsomycin · 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 | 737 | 0.85 | 0.90 | 59 | empty |
| 2 | 1022 | 0.85 | 0.87 | 65 | empty |
| 3 | 1199 | 0.84 | 0.86 | 73 | empty |
| 4 | 452 | 0.81 | 0.90 | 47 | empty |
| 5 | 834 | 0.81 | 0.84 | 56 | empty |
Compared structures
- 1NJN · 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
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1NJN · PDBe 1NJN
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.