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Crystal structure of phosphofructokinase from trypanosoma brucei in complex with an allosteric inhibitor CTCB405
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
- 6QU4
- Type
- protein
- Length
- 1,795 residues
- Chains
- 4
- 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
- JJ2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 456 | 40% helix, 17% strand | O15648 |
| B | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 439 | 42% helix, 17% strand | O15648 |
| C | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 461 | 40% helix, 17% strand | O15648 |
| D | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 439 | 41% helix, 18% strand | O15648 |
Ligands and binding sites
- JJ2 · 1-[(3,4-dichlorophenyl)methyl]-5-[2-(dimethylamino) ethyl]pyrrolo[3,2-c]pyridin-4-one · ligand · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.82 | 0.84 | 84 | empty |
| 2 | 951 | 0.82 | 0.84 | 78 | empty |
| 3 | 1195 | 0.81 | 0.82 | 143 | JJ2, CIT |
| 4 | 1175 | 0.78 | 0.80 | 134 | JJ2, CIT |
| 5 | 348 | 0.73 | 0.85 | 42 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3256 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 3209 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1384 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1121 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 822 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6QU4 · Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an… · 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 0.93
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 6QU4 · PDBe 6QU4 · UniProt O15648
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