MolNFT v1 · #140705 · protein

Crystal structure of tribolium castaneum PINK1 kinase domain in complex with AMP-pnp

5YJ9 · SERINE/THREONINE-protein kinase PINK1, mitochondrial-like…: “Crystal structure of tribolium castaneum PINK1 kinase domain in complex with AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 3 pockets (best druggability 0.60). MolNFT…

PDB: 5YJ9
Type: protein
Length: 343 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase PINK1, mitochondrial-like protein
UniProt: D6WMX4
Ligands: ANP, MG
Pockets: 3 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	SERINE/THREONINE-protein kinase PINK1, mitochondrial-like protein	protein	343	36% helix, 15% strand	D6WMX4

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains D
MG · Magnesium ion · metal · 2 copies · chains D

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

Pockets

3 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	334	0.60	0.77	44	ANP, MG
2	68	0.31	0.74	16	empty
3	64	0.29	0.73	15	empty

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

5YJ9 · Crystal structure of Tribolium castaneum PINK1 kinase domain in complex with AMP-PNP · the same entry in another collection · chain D against D, TM-score 1.00

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 D6WMX4
Elsewhere: RCSB PDB 5YJ9 · PDBe 5YJ9 · UniProt D6WMX4

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