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Crystallization of the thermotoga maritima lysine riboswitch bound to lysine, K+ anomalous data

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: 3DIX
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: 8 · best druggability 0.69

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 · 5 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

8 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	469	0.69	0.81	30	empty
2	520	0.67	0.79	42	NA
3	314	0.50	0.74	18	empty
4	323	0.49	0.73	23	empty
5	110	0.47	0.80	15	empty

Modifications

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

Compared structures

3DIX · Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, K+… · 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 3DIX · PDBe 3DIX

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