MolNFT v1 · #153340 · RNA
Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)
6JBG · RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP…: “Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog…”. X-ray diffraction, 1 ligand (S81), 2 pockets (best…
- PDB
- 6JBG
- Type
- RNA
- Length
- 90 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C) -3'); RNA…
- Ligands
- S81
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C) -3') | rna | 22 | — | — |
| C, D | RNA (5'- R(*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
- S81 · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2, 6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucopyranoside · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.72 | 0.78 | 46 | empty |
| 2 | 848 | 0.69 | 0.76 | 45 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1012 Ų buried · 108 hydrogen bonds · nucleic-nucleic
- A–B · 973 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–C · 186 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- B–D · 114 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 6JBG · 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 6JBG · PDBe 6JBG
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