Research workbench

Crystallization of the thermotoga maritima lysine riboswitch bound to N6-1-iminoethyl-L-lysine

Analyse Crystallization of the thermotoga maritima lysine riboswitch bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DIR
Type: RNA
Length: 174 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (174-mer)
Ligands: IEL, NA, K
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (174-mer)	rna	174	—	—

Ligands and binding sites

IEL · N~6~-[(1Z)-ethanimidoyl]-L-lysine · ligand · chains A
NA · Sodium ion · metal · 11 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

7 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	959	0.71	0.77	56	NA
2	770	0.71	0.78	44	NA
3	348	0.50	0.73	25	NA
4	293	0.50	0.74	19	empty
5	109	0.37	0.76	16	empty

Modifications

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

Compared structures

3DIR · Crystallization of the Thermotoga maritima lysine riboswitch bound to… · 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 3DIR · PDBe 3DIR

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.