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Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of rb+ 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: 4E8P
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, RB
Pockets: 18 · best druggability 0.72

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 · 27 copies · chains A
RB · Rubidium ion · metal · 18 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A

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

Pockets

18 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	924	0.72	0.77	64	MG, RB
2	548	0.70	0.80	45	MG
3	747	0.66	0.76	49	MG, RB, EPE
4	315	0.64	0.82	30	MG
5	391	0.64	0.80	23	MG

Compared structures

4E8P · 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 4E8P · PDBe 4E8P

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