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Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of tl+ and MG2+

Analyse Structure of oceanobacillus iheyensis group II intron in a ligand-free state in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E8Q
Type: RNA
Length: 392 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron
Ligands: SPM, MG, TL
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	392	—	—

Ligands and binding sites

SPM · Spermine · ligand · chains A
MG · Magnesium ion · metal · 30 copies · chains A
TL · Thallium (I) ion · metal · 17 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	929	0.76	0.80	64	MG
2	425	0.68	0.81	36	TL, MG
3	848	0.68	0.75	61	TL, MG
4	671	0.65	0.76	61	TL, MG
5	608	0.61	0.74	36	TL, MG

Compared structures

4E8Q · Structure of Oceanobacillus iheyensis group II intron in a ligand-free state 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 4E8Q · PDBe 4E8Q

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