Research workbench

Duplex [5'-D(GCGTA+TACGC)]2 with incorporated 2'-O-methoxyethyl ribonucleoside

Analyse Duplex [5'-D(GCGTA+TACGC)]2 with incorporated 2'-O-methoxyethyl ribonucleoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 411D
Type: DNA
Length: 20 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*GP*TP*AP*(T39)P*AP*CP*GP*C)-3')
Pockets: 1 · best druggability 0.24

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(GPCPGPTPAP(T39)PAPCPGPC)-3')	dna	10	—	—

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	63	0.24	0.71	12	empty

Interfaces

1 interface between chains.

A–B · 499 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

411D · Duplex [5'-D(GCGTA+TACGC)]2 with incorporated 2'-O-methoxyethyl ribonucleoside · 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 411D · PDBe 411D

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