MolNFT v1 · #49730 · RNA
SAM-II riboswitch bound to S-adenosylmethionine
2QWY: “SAM-II riboswitch bound to S-adenosylmethionine”. X-ray diffraction, 4 ligands (SAM, CS, MG), 4 pockets (best druggability 0.52). MolNFT v1 #49730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2QWY
- Type
- RNA
- Length
- 156 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-II riboswitch
- Ligands
- SAM, CS, MG, PO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | SAM-II riboswitch | rna | 52 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- CS · Cesium ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.52 | 0.74 | 33 | CS, SAM |
| 2 | 374 | 0.52 | 0.73 | 35 | SAM |
| 3 | 265 | 0.47 | 0.74 | 22 | SAM |
| 4 | 59 | 0.27 | 0.74 | 11 | CS |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 2QWY · SAM-II riboswitch bound to S-adenosylmethionine · 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 2QWY · PDBe 2QWY
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