Research workbench
Pyruvate kinase (pyk) from trypanosoma brucei in the presence of magnesium, pep and F26BP
Analyse Pyruvate kinase (pyk) from trypanosoma brucei in the presence of magnesium, pep… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYV
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase 1
- EC
- 2.7.1.40
- UniProt
- P30615
- Ligands
- PEP, FDP, MG, K, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate kinase 1 (EC 2.7.1.40) | protein | 498 | 41% helix, 22% strand | P30615 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- 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
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.78 | 0.85 | 58 | empty |
| 2 | 723 | 0.76 | 0.81 | 77 | MG, PEP |
| 3 | 663 | 0.71 | 0.78 | 74 | MG, K, PEP |
| 4 | 465 | 0.66 | 0.79 | 52 | empty |
| 5 | 272 | 0.58 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2704 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4HYV · Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium, PEP 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 0.97
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 4HYV · PDBe 4HYV · UniProt P30615
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