MolNFT v1 · #13455 · RNA

Crystal structure of tobramycin bound to the eubacterial 16S rRNA a site

1LC4 · 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP…: “Crystal structure of tobramycin bound to the eubacterial 16S rRNA a site”. X-ray diffraction, 1 ligand (TOY), 1 pocket (best druggability 0.47). MolNFT v1 #13455 on…

PDB: 1LC4
Type: RNA
Length: 42 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP *GP*UP*CP*GP*C)-3'
Ligands: TOY
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'-R(UPUPGPCPGPUPCPAPCPAPCPCPGPGPUPGPAPAP GPUPCPGP*C)-3'	rna	21	—	—

Ligands and binding sites

TOY · Tobramycin · ligand · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.47	0.73	24	empty

Interfaces

1 interface between chains.

A–B · 999 Å² buried · 106 hydrogen bonds · nucleic-nucleic

Compared structures

1LC4 · Crystal Structure of Tobramycin Bound to the Eubacterial 16S rRNA A Site · 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 1LC4 · PDBe 1LC4

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