Research workbench
Crystal structure of pyruvate kinase from leishmania mexicana in complex with sulphate ions
Analyse Crystal structure of pyruvate kinase from leishmania mexicana 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
- 3E0V
- Type
- protein
- Length
- 2,971 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate kinase (EC 2.7.1.40) | protein | 494 | 39% helix, 20% strand | Q27686 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 497 | 37% helix, 20% strand | Q27686 |
| D, E | Pyruvate kinase (EC 2.7.1.40) | protein | 495 | 40% helix, 20% strand | Q27686 |
| F | Pyruvate kinase (EC 2.7.1.40) | protein | 496 | 38% helix, 20% strand | Q27686 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 40 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.84 | 0.95 | 29 | SO4 |
| 2 | 269 | 0.84 | 0.95 | 27 | SO4 |
| 3 | 252 | 0.83 | 0.94 | 28 | SO4 |
| 4 | 977 | 0.76 | 0.79 | 111 | empty |
| 5 | 989 | 0.76 | 0.79 | 90 | SO4 |
Interfaces
5 interfaces between chains.
- E–F · 2730 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2685 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2658 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1110 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1039 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3E0V · Crystal structure of pyruvate kinase from Leishmania mexicana in complex with sulphate… · the same entry in another collection · chain F against F, 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 0.94
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 3E0V · PDBe 3E0V · UniProt Q27686
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