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Structure of 23S rRNA of the large ribosomal subunit from deinococcus radiodurans in complex with the macrolide erythromycylamine

Analyse Structure of 23S rRNA of the large ribosomal subunit from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O43
Type: RNA
Length: 2,766 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA
Ligands: ERN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2766	—	—

Ligands and binding sites

ERN · (3R,4S,5S,6R,7R,9R,10S,11S,12R,13S,14R)-10-amino-6-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyltetrahydro-2H-py ran-2-yl]oxy}-14-ethyl-7,12,13-trihydroxy-4-{[(2R,4R,5S,6S)-5-hydroxy-4-methoxy-4,6-dimethyltetrahydro-2H-pyran-2-yl]oxy }-3,5,7,9,11,13-hexamethyloxacyclotetradecan-2-one · ligand · 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.86	0.88	86	empty
2	1000	0.85	0.87	73	empty
3	877	0.84	0.87	75	empty
4	947	0.84	0.86	78	empty
5	911	0.83	0.86	55	empty

Compared structures

2O43 · Structure of 23S rRNA of the large ribosomal subunit from Deinococcus radiodurans in… · 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 2O43 · PDBe 2O43

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