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Structure of human USP28 bound to Ubiquitin-PA

Analyse Structure of human USP28 bound to Ubiquitin-PA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HEK
Type: protein
Length: 1,063 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.03
Source: Homo sapiens
Molecule: Ubiquitin carboxyl-terminal hydrolase 28; Polyubiquitin-B
EC: 3.4.19.12
UniProt: Q96RU2, P0CG47
Ligands: CL
Pockets: 15 · best druggability 0.73

Structure

x-ray diffraction · resolution 3.03 · 4 distinct chains · 44% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12)	protein	453	48% helix, 23% strand	Q96RU2
B	Polyubiquitin-B	protein	77	23% helix, 32% strand	P0CG47
C	Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12)	protein	459	47% helix, 22% strand	Q96RU2
D	Polyubiquitin-B	protein	74	24% helix, 28% strand	P0CG47

Ligands and binding sites

CL · Chloride ion · ion · chains A
PG4 · Tetraethylene glycol · additive · 2 copies · chains A

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.73	1.00	24	empty
2	139	0.69	0.90	26	empty
3	294	0.63	0.80	33	empty
4	195	0.61	0.82	34	empty
5	249	0.60	0.80	39	empty

Interfaces

3 interfaces between chains.

A–C · 1746 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1506 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1446 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6HEK · Structure of human USP28 bound to ubiquitin-pa · the same entry in another collection · chain A against A, TM-score 1.00
Q96RU2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 28 (Q96RU2) · 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 Q96RU2
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 6HEK · PDBe 6HEK · UniProt Q96RU2 · UniProt P0CG47

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