MolNFT v1 · #116467 · RNA

RNA octamer containing dt

5DEK · RNA oligonucleotide containing dt: “RNA octamer containing dt”. X-ray diffraction, 1 ligand (NCO), 3 pockets (best druggability 0.37). MolNFT v1 #116467 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DEK
Type: RNA
Length: 32 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA oligonucleotide containing dt
Ligands: NCO
Pockets: 3 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA oligonucleotide containing dt	rna	8	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B, 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	113	0.37	0.75	11	empty
2	84	0.29	0.73	12	empty
3	81	0.27	0.72	12	empty

Interfaces

4 interfaces between chains.

C–D · 405 Å² buried · 46 hydrogen bonds · nucleic-nucleic
A–B · 397 Å² buried · 42 hydrogen bonds · nucleic-nucleic
A–C · 89 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–D · 52 Å² buried · 2 hydrogen bonds · nucleic-nucleic

Compared structures

5DEK · RNA octamer containing dT · 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 5DEK · PDBe 5DEK

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.