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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: 2QIZ
Type: protein
Length: 943 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin conjugation factor E4
UniProt: P54860
Ligands: K
Pockets: 7 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 66% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin conjugation factor E4	protein	943	66% helix, 2% strand	P54860

Ligands and binding sites

K · Potassium ion · metal · chains A

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

Pockets

7 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	286	0.64	0.81	45	empty
2	339	0.61	0.78	42	K
3	61	0.49	0.85	20	empty
4	169	0.42	0.74	28	empty
5	67	0.33	0.75	17	empty

Compared structures

2QIZ · 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 0.91

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 2QIZ · PDBe 2QIZ · UniProt P54860

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