Research workbench
Crystal structure of leishmania mexicana pyruvate kinase (lmpyk) in complex with fructose 2,6 bisphosphate
Analyse Crystal structure of leishmania mexicana pyruvate kinase (lmpyk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HQQ
- Type
- protein
- Length
- 11,952 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q27686
- Ligands
- FDP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X | Pyruvate kinase (EC 2.7.1.40) | protein | 498 | 40% helix, 22% strand | Q27686 |
Ligands and binding sites
- FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · ligand · 24 copies · chains A, B, C, D, E, F, G, H, I, M, J, K, L, S, N, O, P, V, Q, R, T, U, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.80 | 0.87 | 40 | empty |
| 2 | 477 | 0.80 | 0.87 | 38 | empty |
| 3 | 467 | 0.79 | 0.87 | 37 | empty |
| 4 | 490 | 0.79 | 0.86 | 38 | empty |
| 5 | 446 | 0.79 | 0.87 | 36 | empty |
Interfaces
41 interfaces between chains.
- V–X · 2352 Ų buried · 14 hydrogen bonds · protein-protein
- L–N · 2331 Ų buried · 19 hydrogen bonds · protein-protein
- K–M · 2313 Ų buried · 19 hydrogen bonds · protein-protein
- A–I · 2313 Ų buried · 8 hydrogen bonds · protein-protein
- Q–S · 2295 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3HQQ · Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK) in complex with Fructose… · the same entry in another collection · chain A against A, TM-score 1.00
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 3HQQ · PDBe 3HQQ · UniProt Q27686
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