Research workbench

PANK3-ADP-PhosphoPantothenate complex

Analyse PANK3-ADP-PhosphoPantothenate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KPZ
Type: protein
Length: 355 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Homo sapiens
Molecule: Pantothenate kinase 3
EC: 2.7.1.33
UniProt: Q9H999
Ligands: PAZ, ADP, MG
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · resolution 2.4 · 1 distinct chain · 44% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pantothenate kinase 3 (EC 2.7.1.33)	protein	355	44% helix, 26% strand	Q9H999

Ligands and binding sites

PAZ · N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanine · ligand · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.72	0.84	35	empty
2	262	0.64	0.82	40	PAZ, ADP, MG
3	258	0.53	0.75	31	empty
4	122	0.49	0.79	15	empty
5	91	0.40	0.77	21	empty

Compared structures

5KPZ · PANK3-ADP-phosphopantothenate 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 0.99

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

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