MolNFT v1 · #151134 · protein

Structure of the catalytic domain of USP28 (insertion deleted) bound to ubiquitin-pa

6HEI · Ubiquitin carboxyl-terminal hydrolase 28,UBIQUITIN…: “Structure of the catalytic domain of USP28 (insertion deleted) bound to ubiquitin-pa”. X-ray diffraction, 1 ligand (AYE), 5 pockets (best druggability 0.71). MolNFT v1 #151134 on…

PDB: 6HEI
Type: protein
Length: 422 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 28,UBIQUITIN carboxyl-terminal hydrolase 28…
EC: 3.4.19.12
UniProt: Q96RU2, P0CG47
Ligands: AYE
Pockets: 5 · best druggability 0.71

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 28,UBIQUITIN carboxyl-terminal hydrolase 28 (EC 3.4.19.12)	protein	346	38% helix, 28% strand	Q96RU2
B	Polyubiquitin-B	protein	76	24% helix, 33% strand	P0CG47

Ligands and binding sites

AYE · prop-2-en-1-amine · ligand · chains A, B
EDO · 1,2-ethanediol · additive · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	338	0.71	0.83	44	empty
2	335	0.62	0.79	40	EDO
3	87	0.39	0.76	21	empty
4	59	0.35	0.78	15	empty
5	89	0.32	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 1300 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6HEI · Structure of the catalytic domain of USP28 (insertion deleted) 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 0.95

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 6HEI · PDBe 6HEI · UniProt Q96RU2 · UniProt P0CG47

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