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

Analyse Crystal structure of the homo sapiens cytoplasmic 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: 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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