MolNFT v1 · #140069 · RNA

Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site in complex with G418

5XZ1 · RNA (5'- R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*…: “Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site in complex with G418”. X-ray diffraction, 1 ligand (GET), 2 pockets (best druggability 0.58).…

PDB: 5XZ1
Type: RNA
Length: 88 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)- 3')
Ligands: GET
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'- R(UPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGPUPCPGPC)- 3')	rna	22	—	—

Ligands and binding sites

GET · Geneticin · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	576	0.58	0.73	38	GET
2	496	0.56	0.73	29	GET

Interfaces

2 interfaces between chains.

C–D · 1009 Å² buried · 96 hydrogen bonds · nucleic-nucleic
A–B · 976 Å² buried · 104 hydrogen bonds · nucleic-nucleic

Compared structures

5XZ1 · Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with… · 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 5XZ1 · PDBe 5XZ1

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