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A processed non-coding RNA regulates a bacterial antiviral system

Analyse A processed non-coding RNA regulates a bacterial antiviral system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XDB
Type: protein + RNA
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxn; Toxi
EC: 3.1.27.3
UniProt: B8X8Z0
Ligands: CO, SO4
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxn (EC 3.1.27.3)	protein	162	40% helix, 24% strand	B8X8Z0
G	Toxi	rna	36	—	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 6 copies · chains A, G
SO4 · Sulfate ion · ion · 4 copies · chains A, G

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.56	0.79	20	CO
2	163	0.53	0.79	20	empty
3	119	0.44	0.78	14	empty
4	54	0.31	0.77	16	empty

Interfaces

1 interface between chains.

A–G · 971 Å² buried · 20 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2XDB · A processed non-coding RNA regulates a bacterial antiviral system · the same entry in another collection · chain A against A, TM-score 1.00
B8X8Z0 · AlphaFold monomer V2.0 prediction for endoribonuclease toxn (B8X8Z0) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt B8X8Z0
Elsewhere: RCSB PDB 2XDB · PDBe 2XDB · UniProt B8X8Z0

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