MolNFT v1 · #115110 · protein

Structure of human parkin G319A

5C9V · E3 ubiquitin-protein ligase parkin: “Structure of human parkin G319A”. X-ray diffraction, 2 ligands (ZN, SO4), 3 pockets (best druggability 0.44). MolNFT v1 #115110 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C9V
Type: protein
Length: 306 residues
Chains: 1
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
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase parkin (EC 6.3.2.-)	protein	306	19% helix, 25% strand	O60260

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A
SO4 · Sulfate ion · ion · 6 copies · chains A
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

3 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	77	0.44	0.81	15	empty
2	64	0.33	0.76	13	empty
3	61	0.28	0.74	17	empty

Compared structures

5C9V · Structure of human Parkin G319A · 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 0.86

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 5C9V · PDBe 5C9V · UniProt O60260

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