Research workbench

Parkin (S65DUBLR0RBR)

Analyse Parkin (S65DUBLR0RBR) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C23
Type: protein
Length: 768 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase parkin
EC: 6.3.2.-
UniProt: O60260
Ligands: ZN, SO4, CL
Pockets: 14 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 ubiquitin-protein ligase parkin (EC 6.3.2.-)	protein	384	20% helix, 26% strand	O60260

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	695	0.67	0.76	60	GOL
2	405	0.65	0.79	49	empty
3	327	0.61	0.78	32	empty
4	74	0.51	0.85	20	empty
5	65	0.50	0.85	18	empty

Interfaces

1 interface between chains.

A–B · 834 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5C23 · Parkin (S65DUblR0RBR) · 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 0.99

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 O60260
Elsewhere: RCSB PDB 5C23 · PDBe 5C23 · UniProt O60260

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