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Structure of the yeast U-box-containing ubiquitin ligase UFD2P

Analyse Structure of the yeast U-box-containing ubiquitin ligase UFD2P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QJ0
Type: protein
Length: 937 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin conjugation factor E4
UniProt: P54860
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin conjugation factor E4	protein	937	64% helix, 2% strand	P54860

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	338	0.58	0.76	35	empty
2	73	0.54	0.87	17	empty
3	145	0.48	0.78	32	empty
4	103	0.46	0.80	15	empty
5	172	0.41	0.73	30	empty

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

2QJ0 · Structure of the yeast U-box-containing ubiquitin ligase Ufd2p · the same entry in another collection · chain A against A, TM-score 1.00
P54860 · AlphaFold monomer V2.0 prediction for E4 ubiquitin-protein ligase UFD2 (P54860) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P54860
Elsewhere: RCSB PDB 2QJ0 · PDBe 2QJ0 · UniProt P54860

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