MolNFT v1 · #90083 · RNA

Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and MG2+

4E8N · Group iic intron: “Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of NH4+ and MG2+”. X-ray diffraction, 3 ligands (SPM, MG, NH4), 16 pockets (best druggability 0.66). MolNFT v1 #90083 on…

PDB: 4E8N
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, NH4
Pockets: 16 · best druggability 0.66

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 · 31 copies · chains A
NH4 · Ammonium ion · ion · 14 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A

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

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.66	0.84	32	MG
2	701	0.65	0.76	59	MG, NH4
3	648	0.65	0.76	42	MG, NH4
4	228	0.62	0.83	24	empty
5	235	0.62	0.82	24	MG

Compared structures

4E8N · 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 4E8N · PDBe 4E8N

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