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Crystallization of the thermotoga maritima lysine riboswitch bound to lysine, iridium hexamine soak

Analyse Crystallization 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: 3DIO
Type: RNA
Length: 174 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (174-mer)
Ligands: IRI, LYS, NA, K
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 16 copies · chains X
LYS · Lysine · ligand · chains X
NA · Sodium ion · metal · 14 copies · chains X
K · Potassium ion · metal · chains X
1PE · Pentaethylene glycol · additive · chains X

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	714	0.72	0.79	53	NA, IRI
2	467	0.69	0.81	32	NA, IRI
3	300	0.50	0.74	19	NA, IRI
4	252	0.45	0.73	20	NA, IRI
5	82	0.39	0.79	13	IRI

Modifications

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

Compared structures

3DIO · Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM… · the same entry in another collection · chain X against X, 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 3DIO · PDBe 3DIO

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