Research workbench
Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium and F26BP
Analyse Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYW
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Trypanosoma brucei brucei
- Molecule
- Pyruvate kinase 1
- EC
- 2.7.1.40
- UniProt
- P30615
- Ligands
- FDP, MG, K, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.35 · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pyruvate kinase 1 (EC 2.7.1.40) | protein | 498 | 40% helix, 22% strand | P30615 |
| A | Pyruvate kinase 1 (EC 2.7.1.40) | protein | 496 | 40% helix, 21% strand | P30615 |
Ligands and binding sites
- FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · sugar · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
- K · Potassium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.80 | 0.82 | 87 | empty |
| 2 | 690 | 0.72 | 0.79 | 73 | MG, K |
| 3 | 701 | 0.70 | 0.77 | 80 | MG, K |
| 4 | 457 | 0.66 | 0.79 | 55 | empty |
| 5 | 319 | 0.57 | 0.76 | 45 | FDP |
Interfaces
1 interface between chains.
- B–A · 2629 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4HYW · Pyruvate kinase (pyk) from trypanosoma brucei in the presence of magnesium and F26BP · the same entry in another collection · chain A against A, TM-score 1.00
- P30615 · AlphaFold monomer V2.0 prediction for pyruvate kinase 1 (P30615) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P30615
- Elsewhere: RCSB PDB 4HYW · PDBe 4HYW · UniProt P30615
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