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The structure of the thermobifida fusca guanidine III riboswitch with agmatine.
Analyse The structure of the thermobifida fusca guanidine III riboswitch with agmatine. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O69
- Type
- RNA
- Length
- 78 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (41-mer); RNA (37-mer)
- Ligands
- AG2, MG
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (41-mer) | rna | 41 | — | — |
| B | RNA (37-mer) | rna | 37 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.56 | 0.81 | 13 | empty |
| 2 | 169 | 0.49 | 0.78 | 12 | AG2 |
| 3 | 73 | 0.30 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5O69 · The structure of the thermobifida fusca guanidine III riboswitch with agmatine. · 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 5O69 · PDBe 5O69
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