Research workbench
Crystal structure of ATP-bound phosphofructokinase from trypanosoma brucei
Analyse Crystal structure of ATP-bound phosphofructokinase from trypanosoma brucei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F5M
- Type
- protein
- Length
- 1,839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase)
- EC
- 2.7.1.11
- UniProt
- O15648
- Ligands
- ATP, NA, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase) (EC 2.7.1.11) | protein | 458 | 42% helix, 19% strand | O15648 |
| B | 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase) (EC 2.7.1.11) | protein | 462 | 41% helix, 19% strand | O15648 |
| C | 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase) (EC 2.7.1.11) | protein | 461 | 41% helix, 19% strand | O15648 |
| D | 6-phospho-1-fructokinase (ATP-dependent phosphofructokinase) (EC 2.7.1.11) | protein | 458 | 41% helix, 19% strand | O15648 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- SO4 · Sulfate ion · ion · chains B, C
- GOL · Glycerol · additive · 2 copies · chains A, C
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 | 927 | 0.87 | 0.89 | 96 | empty |
| 2 | 913 | 0.85 | 0.87 | 86 | empty |
| 3 | 879 | 0.82 | 0.84 | 91 | ATP, MG |
| 4 | 619 | 0.81 | 0.86 | 65 | ATP, SO4 |
| 5 | 757 | 0.80 | 0.84 | 75 | ATP, MG |
Interfaces
6 interfaces between chains.
- A–B · 3252 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3206 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1346 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1333 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 814 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3F5M · Crystal Structure of ATP-Bound Phosphofructokinase from Trypanosoma brucei · the same entry in another collection · chain D against D, TM-score 1.00
- O15648 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase (O15648) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 O15648
- Elsewhere: RCSB PDB 3F5M · PDBe 3F5M · UniProt O15648
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