Research workbench

PANK3 complex with compound PZ-2891

Analyse PANK3 complex with compound PZ-2891 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B3V
Type: protein
Length: 352 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.601
Source: Homo sapiens
Molecule: Pantothenate kinase 3
EC: 2.7.1.33
UniProt: Q9H999
Ligands: ANP, 7DQ, MG
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · resolution 1.601 · 1 distinct chain · 44% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pantothenate kinase 3 (EC 2.7.1.33)	protein	352	44% helix, 27% strand	Q9H999

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
7DQ · 6-(4-{[4-(propan-2-yl)phenyl]acetyl}piperazin-1-yl) pyridazine-3-carbonitrile · ligand · chains A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	282	0.69	0.83	32	empty
2	259	0.66	0.83	42	ANP, MG, EDO
3	245	0.54	0.76	34	empty
4	102	0.48	0.80	14	empty

Compared structures

6B3V · PANK3 complex with compound pz-2891 · 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 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 Q9H999
Elsewhere: RCSB PDB 6B3V · PDBe 6B3V · UniProt Q9H999

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