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Crystal structure of the bacterial A1408ME1A-mutant ribosomal decoding site in complex with paromomycin

Analyse Crystal structure of the bacterial A1408ME1A-mutant ribosomal decoding site in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZEJ
Type: RNA
Length: 44 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*(1MA) P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
Ligands: PAR
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (5'-R(PUPGPCPGPUPCP(1MA) PCPGPUPCPGPAPCPGPAPAPGPUPCPGPC)-3')	rna	22	—	—

Ligands and binding sites

PAR · Paromomycin · ligand · 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	698	0.61	0.73	37	PAR

Interfaces

1 interface between chains.

A–B · 992 Å² buried · 96 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5ZEJ · Crystal structure of the bacterial A1408me1A-mutant ribosomal decoding site in complex… · 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 5ZEJ · PDBe 5ZEJ

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