MolNFT v1 · #75408 · protein
Crystal structure of leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.
3PP7: “Crystal structure of leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of…”. X-ray diffraction, 3 ligands (PTK, SVR, K), 12 pockets (best druggability 0.80). MolNFT v1 #75408 on GenesisL1: 3D…
- PDB
- 3PP7
- Type
- protein
- Length
- 986 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- PTK, SVR, K
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 492 | 41% helix, 22% strand | Q27686 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 494 | 41% helix, 22% strand | Q27686 |
Ligands and binding sites
- PTK · pyrene-1,3,6,8-tetrasulfonic acid · ligand · chains A
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · chains B
- K · Potassium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.80 | 0.90 | 34 | empty |
| 2 | 617 | 0.69 | 0.78 | 70 | GOL, K |
| 3 | 471 | 0.68 | 0.79 | 48 | K, GOL |
| 4 | 277 | 0.55 | 0.76 | 24 | empty |
| 5 | 218 | 0.52 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2281 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3PP7 · Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug… · the same entry in another collection · chain A against A, TM-score 1.00
- Q27686 · AlphaFold monomer V2.0 prediction for pyruvate kinase (Q27686) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q27686
- Elsewhere: RCSB PDB 3PP7 · PDBe 3PP7 · UniProt Q27686
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