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Crystal structure and improved antisense properties of 2'-O-(2- methoxyethyl)-RNA

Analyse Crystal structure and improved antisense properties of 2'-O-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 469D
Type: RNA
Length: 24 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*(C43)P*(G48)P*(C43)P*(G48)P*(A44)P*(A44)P*(U36)…
Ligands: MG
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (5'-R((C43)P(G48)P(C43)P(G48)P(A44)P(A44)P(U36) P(U36)P(C43)P(G48)P(C43)P(G48))-3')	rna	12	—	—

Ligands and binding sites

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	407	0.57	0.75	22	empty

Interfaces

1 interface between chains.

A–B · 753 Å² buried · 63 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 24 modified (nucleotide modification).

Compared structures

469D · Crystal structure and improved antisense properties of 2'-O-(2-methoxyethyl)-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 469D · PDBe 469D

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