Research workbench
Pyruvate kinase (pyk) from trypanosoma brucei soaked with oxalate
Analyse Pyruvate kinase (pyk) from trypanosoma brucei soaked with oxalate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KCW
- 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
- OXL, FDP, MG, K
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate kinase 1 (EC 2.7.1.40) | protein | 498 | 40% helix, 22% strand | P30615 |
Ligands and binding sites
- OXL · Oxalate ion · 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
- GOL · Glycerol · additive · 3 copies · chains B
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 | 899 | 0.80 | 0.82 | 91 | empty |
| 2 | 811 | 0.76 | 0.81 | 78 | OXL |
| 3 | 686 | 0.70 | 0.78 | 74 | MG, K, OXL, GOL |
| 4 | 489 | 0.67 | 0.79 | 58 | GOL |
| 5 | 128 | 0.48 | 0.79 | 23 | FDP |
Interfaces
1 interface between chains.
- A–B · 2726 Ų buried · 19 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 4KCW · PDBe 4KCW · UniProt P30615
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