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Structure of oceanobacillus iheyensis group II intron in the presence of K+, CA2+ and 5'-exon

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

PDB: 4FAQ
Type: RNA
Length: 395 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Group iic intron
Ligands: SPM, CA, K
Pockets: 17 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Group iic intron	rna	395	—	—

Ligands and binding sites

SPM · Spermine · ligand · 2 copies · chains A
CA · Calcium ion · metal · 24 copies · chains A
K · Potassium ion · metal · 20 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 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	747	0.66	0.76	53	CA, K
2	236	0.65	0.84	29	CA
3	266	0.64	0.83	23	CA
4	627	0.63	0.75	37	K
5	640	0.62	0.75	35	CA, K

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

4FAQ · Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and… · 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 4FAQ · PDBe 4FAQ

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