Research workbench
Apo crystal structure of leishmania MEXICANA(LMPYK)PYRUVATE kinase
Analyse Apo crystal structure of leishmania MEXICANA(LMPYK)PYRUVATE kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQN
- Type
- protein
- Length
- 985 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- K, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 493 | 42% helix, 23% strand | Q27686 |
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 492 | 42% helix, 22% strand | Q27686 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains D, A
- SO4 · Sulfate ion · ion · 2 copies · chains D, A
- GOL · Glycerol · additive · 3 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.82 | 0.95 | 29 | empty |
| 2 | 529 | 0.67 | 0.78 | 53 | GOL |
| 3 | 543 | 0.67 | 0.78 | 54 | K |
| 4 | 244 | 0.54 | 0.77 | 26 | empty |
| 5 | 226 | 0.52 | 0.77 | 23 | GOL |
Interfaces
1 interface between chains.
- D–A · 2286 Ų buried · 17 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 3HQN · PDBe 3HQN · UniProt Q27686
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