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Co-crystallization showing exon recognition by a group II intron

Analyse Co-crystallization showing exon recognition by a 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: 3EOG
Type: RNA
Length: 393 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron; 5'-R(*UP*UP*AP*UP*UP*A)-3'
Ligands: MG, K
Pockets: 19 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	387	—	—
B	5'-R(UPUPAPUPUPA)-3'	rna	6	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 31 copies · chains A, B
K · Potassium ion · metal · 11 copies · chains A

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

Pockets

19 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	713	0.77	0.83	59	MG, K
2	715	0.65	0.75	51	MG
3	452	0.64	0.79	31	MG
4	511	0.64	0.77	41	MG
5	589	0.59	0.73	34	MG

Interfaces

1 interface between chains.

A–B · 476 Å² buried · 28 hydrogen bonds · nucleic-nucleic

Compared structures

3EOG · Co-crystallization showing exon recognition by a group II 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 3EOG · PDBe 3EOG

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