Research workbench
Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog
Analyse Crystal structure of the bacterial ribosomal decoding site in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PDQ
- Type
- RNA
- Length
- 46 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- *UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C- 3')
- Ligands
- NMZ, MG
- Pockets
- 1 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'- *UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C- 3') | rna | 23 | — | — |
Ligands and binding sites
- NMZ · (2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy }-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.66 | 0.74 | 40 | MG, NMZ |
Interfaces
1 interface between chains.
- A–B · 1086 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Compared structures
- 4PDQ · Crystal structure of the bacterial ribosomal decoding site in complex with… · 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 4PDQ · PDBe 4PDQ
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