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Structure of the znf ubp domain from deubiquitinating enzyme isopeptidase T (isot)

Analyse Structure of the znf ubp domain from deubiquitinating enzyme isopeptidase T… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2G43
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin carboxyl-terminal hydrolase 5
EC: 3.1.2.15
UniProt: P45974
Ligands: ZN, UNX
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15)	protein	117	13% helix, 20% strand	P45974
B	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15)	protein	113	13% helix, 19% strand	P45974

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 3 copies · chains B

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

Pockets

2 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	68	0.38	0.78	13	empty
2	52	0.32	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 94 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

2G43 · Structure of the ZNF UBP domain from deubiquitinating enzyme isopeptidase T (IsoT) · the same entry in another collection · chain A against A, TM-score 1.00
P45974 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 5 (P45974) · a predicted model of the same protein · chain B against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P45974
Elsewhere: RCSB PDB 2G43 · PDBe 2G43 · UniProt P45974

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