Research workbench
Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.
Analyse Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F2T
- Type
- RNA
- Length
- 109 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN riboswitch
- Ligands
- IRI, FMN, MG, K
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | FMN riboswitch | rna | 109 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 11 copies · chains X
- FMN · Flavin mononucleotide · ligand · chains X
- MG · Magnesium ion · metal · 7 copies · chains X
- K · Potassium ion · metal · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.74 | 0.79 | 43 | FMN, K, MG, IRI |
| 2 | 141 | 0.46 | 0.78 | 16 | IRI |
| 3 | 120 | 0.33 | 0.72 | 14 | MG |
| 4 | 59 | 0.28 | 0.75 | 14 | IRI |
| 5 | 66 | 0.27 | 0.74 | 12 | IRI |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3F2T · Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak. · the same entry in another collection · chain X against X, 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 3F2T · PDBe 3F2T
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