MolNFT v1 · #90091 · RNA

Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and BA2+

4E8V · Group iic intron: “Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of K+ and BA2+”. X-ray diffraction, 3 ligands (BA, MG, K), 15 pockets (best druggability 0.72). MolNFT v1 #90091 on…

PDB: 4E8V
Type: RNA
Length: 388 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron
Ligands: BA, MG, K
Pockets: 15 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	388	—	—

Ligands and binding sites

BA · Barium ion · metal · 42 copies · chains A
MG · Magnesium ion · metal · 5 copies · chains A
K · Potassium ion · metal · 4 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

15 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	826	0.72	0.78	57	MG, BA
2	707	0.71	0.79	43	MG, BA
3	849	0.69	0.76	47	BA, EPE
4	451	0.67	0.80	39	empty
5	367	0.65	0.81	24	BA

Compared structures

4E8V · 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 4E8V · PDBe 4E8V

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