MolNFT v1 · #151659 · protein

PARKINS65N

6HUE · E3 ubiquitin-protein ligase parkin: “PARKINS65N”. X-ray diffraction, 3 ligands (ZN, SO4, CL), 16 pockets (best druggability 0.66). MolNFT v1 #151659 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HUE
Type: protein
Length: 760 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase parkin
EC: 2.3.2.31
UniProt: O60260
Ligands: ZN, SO4, CL
Pockets: 16 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase parkin (EC 2.3.2.31)	protein	378	19% helix, 26% strand	O60260
B	E3 ubiquitin-protein ligase parkin (EC 2.3.2.31)	protein	382	19% helix, 26% strand	O60260

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	618	0.66	0.76	71	GOL
2	293	0.57	0.77	32	empty
3	274	0.55	0.76	34	empty
4	99	0.54	0.84	24	empty
5	70	0.52	0.86	23	empty

Interfaces

1 interface between chains.

A–B · 756 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6HUE · ParkinS65N · 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 B 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 6HUE · PDBe 6HUE · UniProt O60260

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