MolNFT v1 · #124812 · protein

PANK3:PALMITOYL-CoA complex

5KQD · Pantothenate kinase 3: “PANK3:PALMITOYL-CoA complex”. X-ray diffraction, 2 ligands (PKZ, SO4), 4 pockets (best druggability 0.63). MolNFT v1 #124812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KQD
Type: protein
Length: 312 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pantothenate kinase 3
EC: 2.7.1.33
UniProt: Q9H999
Ligands: PKZ, SO4
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pantothenate kinase 3 (EC 2.7.1.33)	protein	312	43% helix, 22% strand	Q9H999

Ligands and binding sites

PKZ · Palmitoyl-CoA · ligand · chains A
SO4 · Sulfate ion · ion · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	461	0.63	0.76	50	empty
2	228	0.52	0.76	37	empty
3	89	0.44	0.80	17	empty
4	153	0.43	0.74	19	empty

Compared structures

5KQD · PANK3:Palmitoyl-CoA complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9H999 · AlphaFold monomer V2.0 prediction for pantothenate kinase 3 (Q9H999) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q9H999
Elsewhere: RCSB PDB 5KQD · PDBe 5KQD · UniProt Q9H999

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