Research workbench
The structure of the complex of the large ribosomal subunit from D. radiodurans with the antibiotic lankacidin
Analyse The structure of the complex of the large ribosomal subunit from D. radiodurans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JQ4
- Type
- RNA
- Length
- 2,883 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; 5S ribosomal RNA
- Ligands
- LC2
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 23S ribosomal RNA | rna | 2765 | — | — |
| B | 5S ribosomal RNA | rna | 118 | — | — |
Ligands and binding sites
- LC2 · N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide · 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 | 716 | 0.86 | 0.91 | 76 | empty |
| 2 | 997 | 0.85 | 0.87 | 89 | empty |
| 3 | 1122 | 0.84 | 0.87 | 74 | empty |
| 4 | 852 | 0.82 | 0.86 | 64 | empty |
| 5 | 482 | 0.81 | 0.89 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
- 3JQ4 · The structure of the complex of the large ribosomal subunit from D. Radiodurans with the… · 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 3JQ4 · PDBe 3JQ4
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