MolNFT v1 · #141644 · RNA

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

5ZEI · RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)…: “Crystal structure of the bacterial A1408ME1A-mutant ribosomal decoding site in complex with geneticin”. X-ray diffraction, 1 ligand (GET), 1 pocket (best druggability 0.56). MolNFT v1 #141644…

PDB: 5ZEI
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*(1MA) P*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')…
Ligands: GET
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'-R(PUPGPCPGPUPCP(1MA) PCPGPUPCPGPAPCPGPAPAPGPUPCPGPC)-3')	rna	22	—	—
B	RNA (5'-R(PGPCPGPUPCP(1MA) PCPGPUPCPGPAPCPGPAPAPGPUPCPGP*C)-3')	rna	21	—	—

Ligands and binding sites

GET · Geneticin · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	506	0.56	0.73	30	GET

Interfaces

1 interface between chains.

A–B · 984 Å² buried · 94 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5ZEI · 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 5ZEI · PDBe 5ZEI

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.