Research workbench

RNA octamer containing 2'-ome, 4'- cbeta-ome U.

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

PDB: 6CY4
Type: RNA
Length: 64 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*(CBV)P*GP*AP*AP*(UOB)P*UP*CP*G)-3')
Pockets: 1 · best druggability 0.32

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	RNA (5'-R((CBV)PGPAPAP(UOB)PUPCPG)-3')	rna	8	—	—

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	120	0.32	0.72	14	empty

Interfaces

12 interfaces between chains.

E–F · 390 Å² buried · 26 hydrogen bonds · nucleic-nucleic
C–D · 387 Å² buried · 27 hydrogen bonds · nucleic-nucleic
G–H · 385 Å² buried · 27 hydrogen bonds · nucleic-nucleic
A–B · 383 Å² buried · 30 hydrogen bonds · nucleic-nucleic
A–D · 114 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

6CY4 · RNA octamer containing 2'-OMe, 4'- Cbeta-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 6CY4 · PDBe 6CY4

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