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Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site complexed with apramycin

Analyse Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2G5K
Type: RNA
Length: 44 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*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP *UP*CP*GP*C)-3'
Ligands: AM2, NCO, MG
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	5'- R(UPUPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGP UPCPGP*C)-3'	rna	22	—	—

Ligands and binding sites

AM2 · Apramycin · ligand · 2 copies · chains A, B
NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.55	0.73	30	AM2, NCO
2	122	0.34	0.73	15	AM2

Interfaces

1 interface between chains.

A–B · 983 Å² buried · 100 hydrogen bonds · nucleic-nucleic

Compared structures

2G5K · Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2G5K · PDBe 2G5K

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