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

Analyse Crystal structure of the bacterial ribosomal decoding site in complex with G418… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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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