MolNFT v1 · #46427 · RNA

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

2O43: “Structure of 23S rRNA of the large ribosomal subunit from deinococcus radiodurans in complex with the…”. X-ray diffraction, 1 ligand (ERN), 20 pockets (best druggability 0.86). MolNFT v1 #46427 on GenesisL1: 3D structure, binding…

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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