MolNFT v1 · #104756 · RNA

Thermoanaerobacter pseudethanolicus C-di-AMP riboswitch

4QK8: “Thermoanaerobacter pseudethanolicus C-di-AMP riboswitch”. X-ray diffraction, 4 ligands (2BA, MG, K), 3 pockets (best druggability 0.64). MolNFT v1 #104756 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QK8
Type: RNA
Length: 122 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-di-AMP riboswitch
Ligands: 2BA, MG, K, SO4
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-di-AMP riboswitch	rna	122	—	—

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 · 4 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	677	0.64	0.75	44	2BA
2	419	0.54	0.73	21	empty
3	213	0.51	0.78	19	empty

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4QK8 · Thermoanaerobacter pseudethanolicus 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 4QK8 · PDBe 4QK8

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