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Structure of oceanobacillus iheyensis group II intron in a ligand-free state in the presence of na+ 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: 4FAX
Type: RNA
Length: 391 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron
Ligands: MG, NA
Pockets: 12 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	391	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 21 copies · chains A
NA · Sodium ion · metal · 8 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A

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

Pockets

12 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	770	0.73	0.80	46	MG
2	1123	0.73	0.77	68	MG
3	645	0.68	0.78	60	MG, NA
4	534	0.65	0.78	29	MG
5	668	0.65	0.76	55	MG, NA

Compared structures

4FAX · 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

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4FAX · PDBe 4FAX

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