Research workbench

Wt-parkin and pub complex

Analyse Wt-parkin and pub complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5N2W
Type: protein
Length: 457 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase PARKIN,E3 ubiquitin-protein ligase parkin; Polyubiquitin-B
EC: 2.3.2.-
UniProt: O60260, P0CG47
Ligands: TMO, 3CN, ZN, CL
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase PARKIN,E3 ubiquitin-protein ligase parkin (EC 2.3.2.-)	protein	382	19% helix, 26% strand	O60260
B	Polyubiquitin-B	protein	75	20% helix, 36% strand	P0CG47

Ligands and binding sites

TMO · trimethylamine oxide · ligand · 2 copies · chains A
3CN · 3-aminopropane · ligand · chains A, B
ZN · Zinc ion · metal · 8 copies · chains A
CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	657	0.71	0.78	57	TMO
2	104	0.42	0.77	22	empty
3	58	0.38	0.80	16	empty
4	92	0.35	0.75	21	empty
5	52	0.29	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1427 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).

Compared structures

5N2W · WT-Parkin and pUB complex · the same entry in another collection · chain A against A, TM-score 1.00
O60260 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase parkin (O60260) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 O60260
Every structure of UniProt P0CG47
Elsewhere: RCSB PDB 5N2W · PDBe 5N2W · UniProt O60260 · UniProt P0CG47

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