MolNFT v1 · #94511 · protein
Pyruvate kinase (pyk) from trypanosoma brucei in the presence of magnesium and F26BP
4HYW · Pyruvate kinase 1: “Pyruvate kinase (pyk) from trypanosoma brucei in the presence of magnesium and F26BP”. X-ray diffraction, 4 ligands (FDP, MG, K), 7 pockets (best druggability 0.80). MolNFT v1 #94511 on GenesisL1: 3D structure…
- PDB
- 4HYW
- Type
- protein
- Length
- 994 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
- FDP, MG, K, CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 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 · ligand · 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 B against B, 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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