Research workbench
Gentamicin C1A a-site complex
Analyse Gentamicin C1A a-site complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BYJ
- Type
- RNA
- Length
- 27 nucleotides
- Chains
- 1
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (16S RNA)
- Ligands
- GE1, GE2, GE3
- Pockets
- 1 · best druggability 0.42
Structure
solution nmr · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (16S RNA) | rna | 27 | — | — |
Ligands and binding sites
- GE1 · 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose · ligand · chains A
- GE2 · 3,5-diamino-cyclohexanol · ligand · chains A
- GE3 · 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.42 | 0.73 | 15 | GE1, GE2, GE3 |
Compared structures
- 1BYJ · Gentamicin C1A a-site complex · 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 1BYJ · PDBe 1BYJ
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