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Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site in presence of paromomycin

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: 2O3W
Type: RNA
Length: 43 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (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: PAR
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains.

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

Ligands and binding sites

PAR · Paromomycin · ligand · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	373	0.51	0.73	22	PAR
2	117	0.34	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 1019 Å² buried · 88 hydrogen bonds · nucleic-nucleic

Compared structures

2O3W · Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of… · 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 2O3W · PDBe 2O3W

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