MolNFT v1 · #46421 · RNA

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

2O3W · RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*…: “Crystal structure of the homo sapiens cytoplasmic ribosomal decoding site in presence of paromomycin”. X-ray diffraction, 1 ligand (PAR), 2 pockets (best druggability…

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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