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Crystal structure of the thermotoga maritima lysine riboswitch bound to lysine

Analyse Crystal structure 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: 3DIL
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, K, MG
Pockets: 7 · best druggability 0.73

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 · 29 copies · chains A
K · Potassium ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · chains A
1PE · Pentaethylene glycol · additive · 3 copies · chains A
IPA · Isopropyl alcohol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1054	0.73	0.77	54	NA, K
2	804	0.71	0.78	44	NA, K, 1PE
3	286	0.48	0.74	17	empty
4	305	0.48	0.73	25	NA
5	112	0.38	0.76	16	NA

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

3DIL · Crystal structure of the Thermotoga maritima lysine riboswitch bound to lysine · 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 3DIL · PDBe 3DIL

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