Research workbench
Structure of phosphofructokinase from saccharomyces cerevisiae
Analyse Structure of phosphofructokinase from saccharomyces cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O8O
- Type
- protein
- Length
- 6,049 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphofructokinase subunit alpha; 6-phosphofructokinase subunit beta
- EC
- 2.7.1.11
- UniProt
- P16861, P16862
- Ligands
- F6P, FDP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 6-phosphofructokinase subunit alpha (EC 2.7.1.11) | protein | 750 | 46% helix, 18% strand | P16861 |
| B, D, H | 6-phosphofructokinase subunit beta (EC 2.7.1.11) | protein | 763 | 48% helix, 16% strand | P16862 |
| E | 6-phosphofructokinase subunit alpha (EC 2.7.1.11) | protein | 752 | 46% helix, 17% strand | P16861 |
| F | 6-phosphofructokinase subunit beta (EC 2.7.1.11) | protein | 762 | 49% helix, 16% strand | P16862 |
| G | 6-phosphofructokinase subunit alpha (EC 2.7.1.11) | protein | 746 | 46% helix, 17% strand | P16861 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FDP · 2,6-di-O-phosphono-beta-D-fructofuranose · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 989 | 0.86 | 0.87 | 111 | empty |
| 2 | 444 | 0.84 | 0.91 | 82 | empty |
| 3 | 635 | 0.84 | 0.88 | 84 | empty |
| 4 | 376 | 0.83 | 0.92 | 44 | empty |
| 5 | 523 | 0.82 | 0.89 | 86 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2595 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 2560 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 2468 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 2465 Ų buried · 46 hydrogen bonds · protein-protein
- E–H · 586 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3O8O · Structure of phosphofructokinase from Saccharomyces cerevisiae · the same entry in another collection · chain H against H, TM-score 1.00
- P16862 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase subunit beta… · a predicted model of the same protein · chain F against A, TM-score 0.99
- P16861 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase subunit alpha… · a predicted model of the same protein · chain G 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 P16861
- Every structure of UniProt P16862
- Elsewhere: RCSB PDB 3O8O · PDBe 3O8O · UniProt P16861 · UniProt P16862
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