MolNFT v1 · #71639 · protein
Substrate and inhibitor binding to pank
3MK6 · Pantothenate kinase 3: “Substrate and inhibitor binding to pank”. X-ray diffraction, 1 ligand (ACO), 10 pockets (best druggability 0.81). MolNFT v1 #71639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MK6
- Type
- protein
- Length
- 1,401 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantothenate kinase 3
- EC
- 2.7.1.33
- UniProt
- Q9H999
- Ligands
- ACO
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantothenate kinase 3 (EC 2.7.1.33) | protein | 354 | 43% helix, 25% strand | Q9H999 |
| B | Pantothenate kinase 3 (EC 2.7.1.33) | protein | 351 | 43% helix, 25% strand | Q9H999 |
| C | Pantothenate kinase 3 (EC 2.7.1.33) | protein | 351 | 44% helix, 25% strand | Q9H999 |
| D | Pantothenate kinase 3 (EC 2.7.1.33) | protein | 345 | 45% helix, 24% strand | Q9H999 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.82 | 112 | empty |
| 2 | 986 | 0.78 | 0.80 | 101 | ACO, GOL |
| 3 | 913 | 0.77 | 0.80 | 88 | ACO, GOL |
| 4 | 915 | 0.77 | 0.80 | 88 | ACO, GOL |
| 5 | 606 | 0.76 | 0.82 | 75 | ACO |
Interfaces
3 interfaces between chains.
- B–D · 2012 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1983 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 13 hydrogen bonds · protein-protein
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 3MK6 · PDBe 3MK6 · UniProt Q9H999
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