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Crystallization of the thermotoga maritima lysine riboswitch bound to lysine in the absence of MG2+

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

PDB: 3DIZ
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
Pockets: 6 · best druggability 0.72

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 · 12 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

6 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	971	0.72	0.77	54	NA
2	775	0.71	0.78	44	NA
3	263	0.47	0.74	18	empty
4	263	0.46	0.73	23	NA
5	65	0.38	0.80	13	empty

Modifications

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

Compared structures

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

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