MolNFT v1 · #64569 · RNA

Insight into group II intron catalysis from revised crystal structure

3G78: “Insight into group II intron catalysis from revised crystal structure”. X-ray diffraction, 2 ligands (MG, K), 12 pockets (best druggability 0.74). MolNFT v1 #64569 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3G78
Type: RNA
Length: 398 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group II intron; Ligated exon product
Ligands: MG, K
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group II intron	rna	389	—	—
Z	Ligated exon product	rna	9	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 51 copies · chains A, Z
K · Potassium ion · metal · 26 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	554	0.74	0.83	49	MG
2	1140	0.71	0.76	68	MG, K
3	793	0.68	0.76	58	MG, K
4	326	0.67	0.83	29	MG, K
5	288	0.62	0.81	28	MG

Interfaces

1 interface between chains.

A–Z · 535 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Compared structures

3G78 · Insight into group II intron catalysis from revised crystal structure · 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 3G78 · PDBe 3G78

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