MolNFT v1 · #18306 · protein
The structure of leishmania pyruvate kinase
1PKL · Protein (pyruvate kinase): “The structure of leishmania pyruvate kinase”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #18306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PKL
- Type
- protein
- Length
- 3,939 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pyruvate kinase)
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Protein (pyruvate kinase) (EC 2.7.1.40) | protein | 491 | 42% helix, 22% strand | Q27686 |
| B | Protein (pyruvate kinase) (EC 2.7.1.40) | protein | 489 | 42% helix, 21% strand | Q27686 |
| C, H | Protein (pyruvate kinase) (EC 2.7.1.40) | protein | 492 | 40% helix, 22% strand | Q27686 |
| D, E | Protein (pyruvate kinase) (EC 2.7.1.40) | protein | 493 | 41% helix, 22% strand | Q27686 |
| G | Protein (pyruvate kinase) (EC 2.7.1.40) | protein | 498 | 41% helix, 21% strand | Q27686 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.84 | 0.94 | 29 | empty |
| 2 | 248 | 0.83 | 0.95 | 29 | empty |
| 3 | 268 | 0.83 | 0.94 | 29 | empty |
| 4 | 274 | 0.82 | 0.93 | 31 | empty |
| 5 | 568 | 0.73 | 0.81 | 60 | empty |
Interfaces
8 interfaces between chains.
- B–D · 2349 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2323 Ų buried · 15 hydrogen bonds · protein-protein
- F–H · 2312 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 2309 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 930 Ų buried · 20 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 Q27686
- Elsewhere: RCSB PDB 1PKL · PDBe 1PKL · UniProt Q27686
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