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Structure of oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of na+, MG2+ and 5'-exon

Analyse Structure of oceanobacillus iheyensis group II intron U-mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T3S
Type: RNA
Length: 392 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron ribozyme
Ligands: MG, NA
Pockets: 17 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron ribozyme	rna	392	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 20 copies · chains A
NA · Sodium ion · metal · 8 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A

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

Pockets

17 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	654	0.69	0.78	49	MG
2	755	0.66	0.75	45	MG, NA
3	451	0.66	0.79	40	empty
4	644	0.64	0.75	47	MG
5	349	0.63	0.80	21	MG

Compared structures

6T3S · Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6T3S · PDBe 6T3S

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