MolNFT v1 · #76781 · protein
Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with benzothiazole-2,5-disulfonic acid.
3QV8: “Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with benzothiazole-2,5-disulfonic…”. X-ray diffraction, 2 ligands (S62, PO4), 13 pockets (best druggability 0.79). MolNFT v1 #76781 on GenesisL1: 3D…
- PDB
- 3QV8
- Type
- protein
- Length
- 888 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
- S62, PO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 492 | 42% helix, 21% strand | Q27686 |
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 396 | 48% helix, 17% strand | Q27686 |
Ligands and binding sites
- S62 · 1,3-benzothiazole-2,5-disulfonic acid · ligand · 2 copies · chains D, A
- PO4 · Phosphate ion · ion · 4 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.79 | 0.89 | 38 | PO4 |
| 2 | 479 | 0.67 | 0.79 | 53 | S62 |
| 3 | 261 | 0.54 | 0.77 | 24 | empty |
| 4 | 246 | 0.53 | 0.77 | 25 | empty |
| 5 | 176 | 0.48 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- D–A · 2261 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3QV8 · Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with… · the same entry in another collection · chain D against D, 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 3QV8 · PDBe 3QV8 · UniProt Q27686
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