MolNFT v1 · #177286 · RNA

Crystal structure of the bacterial ribosomal decoding site in complex with G418 and HG(II)

7EDL · RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP…: “Crystal structure of the bacterial ribosomal decoding site in complex with G418 and HG(II)”. X-ray diffraction, 2 ligands (GET, HG), 1 pocket (best druggability 0.59).…

PDB: 7EDL
Type: RNA
Length: 43 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C) -3')
Ligands: GET, HG
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'- R(PUPGPCPGPUPCPAPCPGPCPCPGPGPCPGPAPAPGPUPCPGPC) -3')	rna	22	—	—
B	RNA (5'- R(PUPGPCPGPUPCPAPCPGPCPCPGPGPCPGPAPAPGPUPCPGPC) -3')	rna	21	—	—

Ligands and binding sites

GET · Geneticin · ligand · 2 copies · chains A, B
HG · Mercury (II) ion · metal · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	584	0.59	0.74	29	GET

Interfaces

1 interface between chains.

A–B · 1003 Å² buried · 98 hydrogen bonds · nucleic-nucleic

Compared structures

7EDL · Crystal structure of the bacterial ribosomal decoding site in complex with G418 and Hg(II) · 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 7EDL · PDBe 7EDL

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