Research workbench

Tertiary architecture of the oceanobacillus iheyensis group II intron

Analyse Tertiary architecture of the oceanobacillus iheyensis group II intron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IGI
Type: RNA
Length: 396 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron; 5'-R(*CP*GP*CP*UP*CP*UP*AP*CP*UP*CP*UP*AP*U)-3'
Ligands: MG, K
Pockets: 15 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	388	—	—
B	5'-R(CPGPCPUPCPUPAPCPUPCPUPAP*U)-3'	rna	8	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 44 copies · chains A, B
K · Potassium ion · metal · 22 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	353	0.68	0.83	34	MG
2	749	0.67	0.76	52	MG, K
3	239	0.64	0.84	30	MG, K
4	436	0.63	0.78	30	MG
5	637	0.62	0.74	37	MG, K

Interfaces

1 interface between chains.

A–B · 527 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

3IGI · Tertiary Architecture of the Oceanobacillus Iheyensis Group II Intron · the same entry in another collection · chain B against B, 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 3IGI · PDBe 3IGI

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.