MolNFT v1 · #61947 · protein
Crystal structure of pyruvate kinase from leishmania mexicana in complex with sulphate ions
3E0V: “Crystal structure of pyruvate kinase from leishmania mexicana in complex with sulphate ions”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.84). MolNFT v1 #61947 on GenesisL1: 3D structure, binding sites and…
- 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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