MolNFT v1 · #79138 · RNA
Crystal structure of thf riboswitch, bound with 5-formyl-thf
3SUH: “Crystal structure of thf riboswitch, bound with 5-formyl-thf”. X-ray diffraction, 2 ligands (FFO, NA), 5 pockets (best druggability 0.55). MolNFT v1 #79138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3SUH
- Type
- RNA
- Length
- 101 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboswitch
- Ligands
- FFO, NA
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Riboswitch | rna | 101 | — | — |
Ligands and binding sites
- FFO · N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · chains X
- NA · Sodium ion · metal · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.55 | 0.75 | 25 | empty |
| 2 | 368 | 0.51 | 0.73 | 22 | empty |
| 3 | 276 | 0.48 | 0.74 | 22 | NA |
| 4 | 164 | 0.44 | 0.76 | 14 | empty |
| 5 | 110 | 0.39 | 0.76 | 11 | empty |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3SUH · Crystal structure of THF riboswitch, bound with 5-formyl-THF · 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 3SUH · PDBe 3SUH
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