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5 prime exon-free pre-2S intermediate of the tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct

Analyse 5 prime exon-free pre-2S intermediate of the tetrahymena group I intron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R6L
Type: RNA
Length: 366 nucleotides
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group I intron, 5 prime fragment; Group I intron, 3 prime fragment plus 3 prime exon
Ligands: MG
Pockets: 19 · best druggability 0.71

Structure

electron microscopy · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group I intron, 5 prime fragment	rna	343	—	—
B	Group I intron, 3 prime fragment plus 3 prime exon	rna	23	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 20 copies · chains A, B

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	125	0.71	0.92	18	MG
2	733	0.70	0.78	45	MG
3	524	0.66	0.78	47	MG
4	686	0.65	0.75	31	empty
5	378	0.62	0.79	28	MG

Interfaces

1 interface between chains.

A–B · 1495 Å² buried · 89 hydrogen bonds · nucleic-nucleic

Compared structures

7R6L · 5 prime exon-free pre-2S intermediate of the Tetrahymena group I intron… · 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 7R6L · PDBe 7R6L

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