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Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with acid blue 80.
Analyse Crystal structure of leishmania mexicana pyruvate KINASE(LMPYK)IN complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QV6
- Type
- protein
- Length
- 887 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
- QV6, K, PO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 493 | 41% helix, 22% strand | Q27686 |
| D | Pyruvate kinase (EC 2.7.1.40) | protein | 394 | 49% helix, 18% strand | Q27686 |
Ligands and binding sites
- QV6 · 3-({4-[(2,4-dimethyl-5-sulfophenyl)amino]-9,10-dioxo-9,10-dihydroanthracen-1-yl}amino)-2,4,6-trimethylbenzenesulfonic acid · ligand · 2 copies · chains A
- K · Potassium ion · metal · 4 copies · chains A, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.80 | 0.90 | 35 | empty |
| 2 | 584 | 0.69 | 0.79 | 55 | K |
| 3 | 266 | 0.55 | 0.77 | 27 | empty |
| 4 | 231 | 0.53 | 0.77 | 24 | empty |
| 5 | 204 | 0.47 | 0.75 | 29 | PO4 |
Interfaces
1 interface between chains.
- A–D · 2310 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3QV6 · Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue… · 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 D 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 3QV6 · PDBe 3QV6 · UniProt Q27686
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