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RNA octamer containing 2'-F-4'-ome U.

Analyse RNA octamer containing 2'-F-4'-ome U. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VR4
Type: RNA
Length: 32 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
Ligands: CON
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(CPGPAPAP(UMO)PUPCPG)-3')	rna	8	—	—

Ligands and binding sites

CON · Cobalt tetraammine ion · ligand · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.45	0.76	13	empty
2	75	0.27	0.72	11	CON
3	70	0.25	0.72	11	empty

Interfaces

4 interfaces between chains.

A–B · 395 Å² buried · 31 hydrogen bonds · nucleic-nucleic
C–D · 394 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–D · 92 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–C · 60 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

5VR4 · RNA octamer containing 2'-F-4'-OMe U. · 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 5VR4 · PDBe 5VR4

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