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Crystal structure of the homo sapiens cytoplasmic ribosomal decoding a site

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

PDB: 2FQN
Type: RNA
Length: 43 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: NCO, MG
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'- R(UPUPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGP UPCPGP*C)-3'	rna	22	—	—
B	5'- R(UPUPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGP UPCPGP*C)-3'	rna	21	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	251	0.44	0.72	24	NCO
2	152	0.36	0.72	16	MG

Interfaces

1 interface between chains.

A–B · 1007 Å² buried · 85 hydrogen bonds · nucleic-nucleic

Compared structures

2FQN · Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site · 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 2FQN · PDBe 2FQN

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