MolNFT v1 · #170312 · protein

Ring-dtc domains of deltex 2, bound to ADP-ribose

6Y3J · Probable E3 ubiquitin-protein ligase DTX2: “Ring-dtc domains of deltex 2, bound to ADP-ribose”. X-ray diffraction, 2 ligands (APR, ZN), 2 pockets (best druggability 0.47). MolNFT v1 #170312 on GenesisL1: 3D structure, binding sites…

PDB: 6Y3J
Type: protein
Length: 227 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable E3 ubiquitin-protein ligase DTX2
EC: 2.3.2.27
UniProt: Q86UW9
Ligands: APR, ZN
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable E3 ubiquitin-protein ligase DTX2 (EC 2.3.2.27)	protein	227	19% helix, 23% strand	Q86UW9

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

2 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	169	0.47	0.76	24	empty
2	74	0.32	0.75	19	APR

Compared structures

6Y3J · RING-DTC domains of Deltex 2, bound to ADP-ribose · the same entry in another collection · chain A against A, TM-score 1.00
Q86UW9 · AlphaFold monomer V2.0 prediction for probable E3 ubiquitin-protein ligase DTX2 (Q86UW9) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q86UW9
Elsewhere: RCSB PDB 6Y3J · PDBe 6Y3J · UniProt Q86UW9

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