MolNFT v1 · #73579 · protein

Crystal structure of a josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating activity

3O65 · Putative ataxin-3-like protein: “Crystal structure of a josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating…”. X-ray diffraction, 2 ligands (NEH, NA), 13 pockets (best druggability 0.72). MolNFT v1…

PDB: 3O65
Type: protein
Length: 1,031 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative ataxin-3-like protein; Ubiquitin
EC: 3.1.2.15
UniProt: Q9H3M9, P0CG47
Ligands: NEH, NA
Pockets: 13 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Putative ataxin-3-like protein (EC 3.1.2.15)	protein	181	41% helix, 19% strand	Q9H3M9
B, D, F, H	Ubiquitin	protein	75	24% helix, 36% strand	P0CG47
C	Putative ataxin-3-like protein (EC 3.1.2.15)	protein	182	38% helix, 18% strand	Q9H3M9
E	Putative ataxin-3-like protein (EC 3.1.2.15)	protein	187	37% helix, 17% strand	Q9H3M9

Ligands and binding sites

NEH · Ethanamine · ligand · 4 copies · chains A, B, C, D, E, F, G, H
NA · Sodium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.72	0.76	94	NEH
2	137	0.66	0.87	20	empty
3	133	0.62	0.86	24	empty
4	118	0.61	0.86	28	empty
5	162	0.61	0.83	24	empty

Interfaces

9 interfaces between chains.

A–B · 1342 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1322 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1286 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1195 Å² buried · 12 hydrogen bonds · protein-protein
C–G · 762 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 modified, 8 covalent (engineered, covalent ligand).

Compared structures

3O65 · Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3… · the same entry in another collection · chain H against H, TM-score 1.00
Q9H3M9 · AlphaFold monomer V2.0 prediction for ataxin-3-like protein (Q9H3M9) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q9H3M9
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 3O65 · PDBe 3O65 · UniProt Q9H3M9 · UniProt P0CG47

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