MolNFT v1 · #63210 · RNA
Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.
3F2T: “Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.”. X-ray diffraction, 4 ligands (IRI, FMN, MG), 5 pockets (best druggability 0.74). MolNFT v1 #63210 on GenesisL1: 3D structure, binding sites and pockets…
- 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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