Research workbench
Crystal structure of leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.
Analyse Crystal structure of leishmania mexicana pyruvate kinase in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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