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Crystal structure of leishmania mexicana pyruvate kinase (LMPYK)IN complex with 1,3,6,8-pyrenetetrasulfonic acid
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
- 3IS4
- Type
- protein
- Length
- 984 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
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate kinase (EC 2.7.1.40) | protein | 492 | 41% helix, 22% strand | Q27686 |
Ligands and binding sites
- PTK · pyrene-1,3,6,8-tetrasulfonic acid · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.82 | 0.94 | 29 | GOL |
| 2 | 504 | 0.67 | 0.78 | 50 | GOL |
| 3 | 438 | 0.67 | 0.79 | 44 | empty |
| 4 | 268 | 0.55 | 0.77 | 27 | empty |
| 5 | 232 | 0.53 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2319 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3IS4 · Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with… · 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 3IS4 · PDBe 3IS4 · UniProt Q27686
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