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Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine

Analyse Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y1N
Type: RNA
Length: 508 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group II intron, domain 1
Ligands: IRI, MG, K
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group II intron, domain 1	rna	249	—	—
B	Group II intron, domain 1	rna	259	—	—

Ligands and binding sites

IRI · Iridium hexammine ion · ligand · 28 copies · chains A, B
MG · Magnesium ion · metal · 8 copies · chains A, B
K · Potassium ion · metal · chains B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.72	0.77	68	IRI, MG
2	982	0.71	0.76	63	IRI, MG
3	607	0.66	0.77	42	IRI
4	784	0.64	0.74	42	IRI, MG
5	821	0.64	0.74	37	IRI, MG

Interfaces

1 interface between chains.

A–B · 212 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

4Y1N · Oceanobacillus iheyensis group II intron domain 1 with iridium hexamine · 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 4Y1N · PDBe 4Y1N

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