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Structure of ARF1 RNA

Analyse Structure of ARF1 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HU6
Type: RNA
Length: 57 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.904
Molecule: RNA (19-mer); RNA (5'-R(*GP*AP*GP*UP*GP*CP*CP*AP*GP*A)-3'); RNA…
Ligands: NH4
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · resolution 1.904 · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (19-mer)	rna	19	—	—
E	RNA (19-mer)	rna	19	—	—
B	RNA (5'-R(GPAPGPUPGPCPCPAPGPA)-3')	rna	10	—	—
F	RNA (5'-R(CPUPGPGPUPAPCPUP*C)-3')	rna	9	—	—

Ligands and binding sites

NH4 · Ammonium ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	347	0.48	0.72	27	empty

Interfaces

5 interfaces between chains.

A–E · 908 Å² buried · 109 hydrogen bonds · nucleic-nucleic
B–F · 459 Å² buried · 54 hydrogen bonds · nucleic-nucleic
E–F · 92 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–B · 88 Å² buried · 2 hydrogen bonds · nucleic-nucleic
E–B · 83 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

6HU6 · Structure of ARF1 RNA · 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 6HU6 · PDBe 6HU6

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