MolNFT v1 · #119038 · RNA
SAM-I riboswitch bearing the H. marismortui kt-7 variant 3BN is ug
5FK1: “SAM-I riboswitch bearing the H. marismortui kt-7 variant 3BN is ug”. X-ray diffraction, 3 ligands (SAM, BA, NA), 3 pockets (best druggability 0.75). MolNFT v1 #119038 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FK1
- Type
- RNA
- Length
- 94 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-I riboswitch
- Ligands
- SAM, BA, NA
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SAM-I riboswitch | rna | 94 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- BA · Barium ion · metal · 12 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.75 | 0.79 | 54 | SAM, BA, NA |
| 2 | 436 | 0.61 | 0.77 | 23 | BA, NA |
| 3 | 231 | 0.45 | 0.73 | 16 | BA, NA |
Compared structures
- 5FK1 · SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UG · 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 5FK1 · PDBe 5FK1
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