MolNFT v1 · #104758 · RNA
C-di-AMP riboswitch from thermoanaerobacter pseudethanolicus, iridium hexamine soak
4QKA: “C-di-AMP riboswitch from thermoanaerobacter pseudethanolicus, iridium hexamine soak”. X-ray diffraction, 5 ligands (IRI, 2BA, MG), 3 pockets (best druggability 0.65). MolNFT v1 #104758 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QKA
- Type
- RNA
- Length
- 120 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-di-AMP riboswitch
- Ligands
- IRI, 2BA, MG, K, SO4
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-di-AMP riboswitch | rna | 120 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 5 copies · chains A
- 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 · chains A
- K · Potassium ion · metal · chains A
- SO4 · Sulfate ion · ion · 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 | 683 | 0.65 | 0.75 | 44 | 2BA |
| 2 | 213 | 0.52 | 0.78 | 17 | empty |
| 3 | 344 | 0.50 | 0.73 | 21 | IRI |
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4QKA · c-di-AMP riboswitch from Thermoanaerobacter pseudethanolicus, iridium hexamine 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 4QKA · PDBe 4QKA
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