MolNFT v1 · #124800 · protein
PANK3-ADP-phosphopantothenate complex
5KPZ · Pantothenate kinase 3: “PANK3-ADP-phosphopantothenate complex”. X-ray diffraction, 3 ligands (PAZ, ADP, MG), 5 pockets (best druggability 0.72). MolNFT v1 #124800 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KPZ
- Type
- protein
- Length
- 355 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
- PAZ, ADP, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 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.
| Volume (ų) | 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
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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