MolNFT v1 · #146836 · protein
Crystal structure of the pyruvate kinase (PK1) from the mosquito aedes aegypti
6DU6: “Crystal structure of the pyruvate kinase (PK1) from the mosquito aedes aegypti”. X-ray diffraction, 1 ligand (FBP), 20 pockets (best druggability 0.88). MolNFT v1 #146836 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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