MolNFT v1 · #170380 · protein

Ring-dtc domain of DELTEX1

6Y5N · E3 ubiquitin-protein ligase DTX1: “Ring-dtc domain of DELTEX1”. X-ray diffraction, 2 ligands (ZN, CL), 5 pockets (best druggability 0.63). MolNFT v1 #170380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y5N
Type: protein
Length: 455 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase DTX1
EC: 2.3.2.27
UniProt: Q86Y01
Ligands: ZN, CL
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase DTX1 (EC 2.3.2.27)	protein	228	20% helix, 22% strand	Q86Y01
B	E3 ubiquitin-protein ligase DTX1 (EC 2.3.2.27)	protein	227	19% helix, 22% strand	Q86Y01

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	363	0.63	0.78	29	empty
2	339	0.61	0.78	31	empty
3	371	0.54	0.73	39	CL
4	173	0.43	0.74	23	CL
5	190	0.42	0.73	21	empty

Interfaces

1 interface between chains.

A–B · 827 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6Y5N · RING-DTC domain of Deltex1 · the same entry in another collection · chain A against A, TM-score 1.00
Q86Y01 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase DTX1 (Q86Y01) · a predicted model of the same protein · chain A against A, TM-score 0.85

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 Q86Y01
Elsewhere: RCSB PDB 6Y5N · PDBe 6Y5N · UniProt Q86Y01

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