MolNFT v1 · #128687 · RNA
The structure of the thermobifida fusca guanidine III riboswitch with aminoguanidine
5NY8 · RNA (41-mer): “The structure of the thermobifida fusca guanidine III riboswitch with aminoguanidine”. X-ray diffraction, 3 ligands (AGU, MG, NA), 4 pockets (best druggability 0.53). MolNFT v1 #128687 on GenesisL1: 3D structure…
- PDB
- 5NY8
- Type
- RNA
- Length
- 82 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (41-mer)
- Ligands
- AGU, MG, NA
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (41-mer) | rna | 41 | — | — |
Ligands and binding sites
- AGU · Aminoguanidine · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.53 | 0.81 | 12 | MG |
| 2 | 130 | 0.46 | 0.79 | 14 | AGU |
| 3 | 53 | 0.26 | 0.75 | 9 | empty |
| 4 | 63 | 0.24 | 0.72 | 11 | empty |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5NY8 · The structure of the thermobifida fusca guanidine III riboswitch with aminoguanidine · 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 5NY8 · PDBe 5NY8
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