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Post-2S intermediate of the tetrahymena group I intron, symmetry- expanded monomer from a synthetic dimeric construct

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

PDB: 7R6M
Type: RNA
Length: 362 nucleotides
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group I intron; Ligated exon mimic of the group I intron
Ligands: MG
Pockets: 14 · best druggability 0.74

Structure

electron microscopy · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group I intron	rna	356	—	—
B	Ligated exon mimic of the group I intron	rna	6	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 13 copies · chains A

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

Pockets

14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1113	0.74	0.78	68	MG
2	147	0.72	0.92	16	MG
3	881	0.69	0.76	44	MG
4	924	0.68	0.75	47	MG
5	873	0.67	0.75	32	empty

Interfaces

1 interface between chains.

A–B · 479 Å² buried · 29 hydrogen bonds · nucleic-nucleic

Compared structures

7R6M · Post-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a… · 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 7R6M · PDBe 7R6M

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