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Crystal structure of a 14BP RNA oligonucleotide containing double uu bulges: a novel intramolecular U*(AU) base triple

Analyse Crystal structure of a 14BP RNA oligonucleotide containing double uu bulges: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FUF
Type: RNA
Length: 28 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: (5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*C)-3')
Ligands: SPM, MG
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	(5'-R(GPGPUPAPUPUPUPCPGPGPUPAP(CBR)PC)-3')	rna	14	—	—

Ligands and binding sites

SPM · Spermine · ligand · chains A, B
MG · Magnesium ion · metal · 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	278	0.58	0.79	26	MG, SPM

Interfaces

1 interface between chains.

A–B · 897 Å² buried · 66 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1FUF · Crystal structure of a 14BP RNA oligonucleotide containing double uu bulges: a novel… · 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 1FUF · PDBe 1FUF

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