MolNFT v1 · #140998 · protein

Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin

5YT6: “Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.81). MolNFT v1 #140998 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YT6
Type: protein
Length: 434 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin; TAX1-binding protein 1
UniProt: P0CG47, Q86VP1
Ligands: ZN, SO4
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 26% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, C, G	Ubiquitin	protein	75	24% helix, 37% strand	P0CG47
F, B	TAX1-binding protein 1	protein	35	29% helix, 11% strand	Q86VP1
A	Ubiquitin	protein	75	24% helix, 37% strand	P0CG47
D	TAX1-binding protein 1	protein	31	29% helix, 13% strand	Q86VP1
H	TAX1-binding protein 1	protein	33	27% helix, 12% strand	Q86VP1

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains F, B, D, H
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
GOL · Glycerol · additive · chains G, H
EDO · 1,2-ethanediol · additive · chains G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.81	0.82	89	empty
2	114	0.43	0.77	18	empty
3	95	0.32	0.73	16	SO4
4	71	0.28	0.73	13	empty
5	70	0.28	0.73	17	empty

Interfaces

17 interfaces between chains.

G–H · 495 Å² buried · 1 hydrogen bond · protein-protein
A–B · 477 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 463 Å² buried · 1 hydrogen bond · protein-protein
F–G · 459 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 424 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5YT6 · Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin · the same entry in another collection · chain H against H, TM-score 1.00
Q86VP1 · AlphaFold monomer V2.0 prediction for TAX1-binding protein 1 (Q86VP1) · a predicted model of the same protein · chain H 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 P0CG47
Every structure of UniProt Q86VP1
Elsewhere: RCSB PDB 5YT6 · PDBe 5YT6 · UniProt P0CG47 · UniProt Q86VP1

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