MolNFT v1 · #125422 · protein

Structure of USP46-ubvme

5L8H · Ubiquitin carboxyl-terminal hydrolase 46: “Structure of USP46-ubvme”. X-ray diffraction, 2 ligands (GVE, ZN), 5 pockets (best druggability 0.50). MolNFT v1 #125422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L8H
Type: protein
Length: 386 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: GVE, ZN
Pockets: 5 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.4.19.12)	protein	311	31% helix, 37% strand	P62068
B	Polyubiquitin-B	protein	75	24% helix, 32% strand	P0CG47

Ligands and binding sites

GVE · Methyl 4-aminobutanoate · ligand · chains A, B
ZN · Zinc ion · metal · chains A

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

Pockets

5 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	119	0.50	0.80	19	empty
2	141	0.49	0.79	21	empty
3	57	0.33	0.77	15	empty
4	79	0.32	0.74	16	empty
5	65	0.29	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 1904 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5L8H · Structure of USP46-UbVME · 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 5L8H · PDBe 5L8H · UniProt P62068 · UniProt P0CG47

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