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Crystal structure of a eukaryotic group II intron lariat

Analyse Crystal structure of a eukaryotic group II intron lariat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R0D
Type: RNA
Length: 630 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iib intron lariat; Ligated exons
Ligands: IRI, SPM, MG, NA
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iib intron lariat	rna	616	—	—
B	Ligated exons	rna	14	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 38 copies · chains A
SPM · Spermine · ligand · 2 copies · chains A
MG · Magnesium ion · metal · 83 copies · chains A, B
NA · Sodium ion · metal · 16 copies · chains A

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.74	0.81	49	IRI, MG
2	724	0.73	0.80	60	MG, NA
3	936	0.71	0.77	60	IRI, MG
4	901	0.67	0.75	39	IRI, MG
5	549	0.67	0.78	30	IRI, MG

Interfaces

1 interface between chains.

A–B · 1125 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

4R0D · Crystal structure of a eukaryotic group II intron lariat · 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 4R0D · PDBe 4R0D

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