MolNFT v1 · #104757 · RNA
Thermovirga lienii C-di-AMP riboswitch
4QK9: “Thermovirga lienii C-di-AMP riboswitch”. X-ray diffraction, 2 ligands (2BA, MG), 4 pockets (best druggability 0.65). MolNFT v1 #104757 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QK9
- Type
- RNA
- Length
- 117 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-di-AMP riboswitch
- Ligands
- 2BA, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-di-AMP riboswitch | rna | 117 | — | — |
Ligands and binding sites
- 2BA · (2r,3r,3as,5r,7ar,9r,10r,10as,12r,14ar)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-D:3', 2'-J][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5, 10,12-tetrol 5,12-dioxide · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 11 copies · chains A
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 | 549 | 0.65 | 0.77 | 25 | empty |
| 2 | 613 | 0.64 | 0.75 | 41 | 2BA |
| 3 | 141 | 0.36 | 0.73 | 13 | empty |
| 4 | 135 | 0.36 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4QK9 · Thermovirga lienii c-di-AMP riboswitch · 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 4QK9 · PDBe 4QK9
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