Research workbench

1.8 a X-ray crystal structure of apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding a site: RNA construct with 5'-overhang

Analyse 1.8 a X-ray crystal structure of apramycin complex with RNA fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OE8
Type: RNA
Length: 33 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*C)- 3'); RNA (5'…
Ligands: AM2
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (5'-R(GPGPGPCPGPUPCPGPCPUPAPGPUPAPCPC)- 3')	rna	16	—	—
B	RNA (5'- R(CPGPGPUPAPCPUPAPAPAPAPGPUPCPGPCP*C)-3')	rna	17	—	—

Ligands and binding sites

AM2 · Apramycin · ligand · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	460	0.56	0.74	29	AM2

Interfaces

1 interface between chains.

A–B · 765 Å² buried · 67 hydrogen bonds · nucleic-nucleic

Compared structures

2OE8 · 1.8 A X-ray crystal structure of Apramycin complex with RNA fragment… · 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 2OE8 · PDBe 2OE8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.