Research workbench
Crystallization of the thermotoga maritima lysine riboswitch bound to lysine, MN2+ soak
Analyse Crystallization of the thermotoga maritima lysine riboswitch bound to lysine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DIY
- Type
- RNA
- Length
- 174 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (174-mer)
- Ligands
- LYS, NA, MN, K
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (174-mer) | rna | 174 | — | — |
Ligands and binding sites
- LYS · Lysine · ligand · chains A
- NA · Sodium ion · metal · 8 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.70 | 0.79 | 50 | empty |
| 2 | 436 | 0.68 | 0.81 | 30 | NA |
| 3 | 262 | 0.49 | 0.75 | 18 | empty |
| 4 | 241 | 0.44 | 0.73 | 19 | NA |
| 5 | 69 | 0.37 | 0.79 | 13 | empty |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3DIY · Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Mn2+ soak · 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 3DIY · PDBe 3DIY
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.