Research workbench

USP46~UBIQUITIN bea covalent complex

Analyse USP46~UBIQUITIN bea covalent complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CVM
Type: protein
Length: 387 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 46; Polyubiquitin-B
EC: 3.4.19.12
UniProt: P62068, P0CG47
Ligands: ZN
Pockets: 4 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.4.19.12)	protein	308	31% helix, 37% strand	P62068
B	Polyubiquitin-B	protein	79	19% helix, 33% strand	P0CG47

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	132	0.48	0.79	22	empty
2	119	0.46	0.78	16	empty
3	74	0.30	0.73	20	empty
4	78	0.30	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 1960 Å² buried · 46 hydrogen bonds · protein-protein

Compared structures

5CVM · USP46~ubiquitin BEA covalent complex · the same entry in another collection · chain A against A, TM-score 1.00
P62068 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 46 (P62068) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P62068
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 5CVM · PDBe 5CVM · UniProt P62068 · UniProt P0CG47

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