MolNFT v1 · #97406 · protein
Pyruvate kinase (pyk) from trypanosoma brucei soaked with oxaloacetate
4KCT · Pyruvate kinase 1: “Pyruvate kinase (pyk) from trypanosoma brucei soaked with oxaloacetate”. X-ray diffraction, 4 ligands (PYR, FDP, MG), 9 pockets (best druggability 0.82). MolNFT v1 #97406 on GenesisL1: 3D structure, binding sites…
- PDB
- 4KCT
- 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
- PYR, FDP, MG, K
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Pyruvate kinase 1 (EC 2.7.1.40) | protein | 498 | 40% helix, 22% strand | P30615 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains B, A
- 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
- GOL · Glycerol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.82 | 0.84 | 122 | empty |
| 2 | 569 | 0.75 | 0.83 | 69 | MG, K, PYR, GOL |
| 3 | 427 | 0.68 | 0.80 | 55 | MG, K, PYR, GOL |
| 4 | 307 | 0.56 | 0.76 | 44 | FDP |
| 5 | 101 | 0.48 | 0.81 | 18 | FDP |
Interfaces
1 interface between chains.
- B–A · 2700 Ų buried · 22 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 P30615
- Elsewhere: RCSB PDB 4KCT · PDBe 4KCT · UniProt P30615
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