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Crystal structure of phosphofructokinase from trypanosoma brucei in complex with an allosteric inhibitor CTCB12
Analyse Crystal structure of phosphofructokinase from trypanosoma brucei in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QU5
- Type
- protein
- Length
- 3,645 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent 6-phosphofructokinase
- EC
- 2.7.1.11
- UniProt
- O15648
- Ligands
- JJ8
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 452 | 40% helix, 18% strand | O15648 |
| B | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 459 | 40% helix, 18% strand | O15648 |
| C | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 461 | 37% helix, 18% strand | O15648 |
| D | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 453 | 40% helix, 18% strand | O15648 |
| E | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 456 | 39% helix, 18% strand | O15648 |
| F | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 456 | 40% helix, 18% strand | O15648 |
| G | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 455 | 38% helix, 18% strand | O15648 |
| H | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 453 | 40% helix, 18% strand | O15648 |
Ligands and binding sites
- JJ8 · 1-[(3,4-dichlorophenyl)methyl]imidazole · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 1120 | 0.85 | 0.86 | 77 | empty |
| 2 | 1022 | 0.85 | 0.86 | 73 | empty |
| 3 | 1077 | 0.85 | 0.86 | 75 | empty |
| 4 | 1069 | 0.85 | 0.85 | 80 | empty |
| 5 | 991 | 0.82 | 0.83 | 119 | empty |
Interfaces
13 interfaces between chains.
- G–H · 3118 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3094 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 3069 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 3060 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1238 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6QU5 · Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an… · the same entry in another collection · chain H against H, TM-score 1.00
- O15648 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase (O15648) · a predicted model of the same protein · chain G 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 6QU5 · PDBe 6QU5 · UniProt O15648
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