Research workbench
Crystal structure of the pyruvate kinase (PK1) from the mosquito aedes aegypti
Analyse Crystal structure of the pyruvate kinase (PK1) from the mosquito aedes aegypti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DU6
- Type
- protein
- Length
- 2,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q16F38
- Ligands
- FBP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 503 | 40% helix, 17% strand | Q16F38 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 509 | 39% helix, 20% strand | Q16F38 |
| C | Pyruvate kinase (EC 2.7.1.40) | protein | 512 | 38% helix, 19% strand | Q16F38 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 505 | 39% helix, 19% strand | Q16F38 |
Ligands and binding sites
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.88 | 0.90 | 138 | empty |
| 2 | 347 | 0.85 | 0.94 | 42 | empty |
| 3 | 119 | 0.80 | 0.97 | 22 | empty |
| 4 | 152 | 0.79 | 0.95 | 36 | empty |
| 5 | 173 | 0.78 | 0.93 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2710 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2684 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1112 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1101 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DU6 · Crystal structure of the pyruvate kinase (PK1) from the mosquito Aedes aegypti · the same entry in another collection · chain A against A, TM-score 1.00
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 Q16F38
- Elsewhere: RCSB PDB 6DU6 · PDBe 6DU6 · UniProt Q16F38
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