MolNFT v1 · #102965 · RNA

Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

4P20 · 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP…: “Crystal structures of the bacterial ribosomal decoding site complexed with amikacin”. X-ray diffraction, 1 ligand (AKN), 1 pocket (best druggability 0.47). MolNFT v1…

PDB: 4P20
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: AKN
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

AKN · (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide · 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	300	0.47	0.73	26	AKN

Interfaces

1 interface between chains.

A–B · 984 Å² buried · 80 hydrogen bonds · nucleic-nucleic

Compared structures

4P20 · Crystal structures of the bacterial ribosomal decoding site complexed with amikacin · 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 4P20 · PDBe 4P20

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