Research workbench
Crystal structure of phosphofructokinase from trypanosoma brucei in complex with an allosteric inhibitor CTCB360
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
- 6QU3
- Type
- protein
- Length
- 1,817 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
- JJ5, SEP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 464 | 41% helix, 16% strand | O15648 |
| B | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 446 | 42% helix, 17% strand | O15648 |
| C | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 446 | 42% helix, 17% strand | O15648 |
| D | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 461 | 41% helix, 16% strand | O15648 |
Ligands and binding sites
- JJ5 · 1-[(3,4-dichlorophenyl)methyl]-7~{H}-pyrrolo[3,2-c]pyridin-4-one · ligand · 4 copies · chains A, B, C, D
- SEP · Phosphoserine · ligand · chains A
- 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.83 | 0.85 | 79 | empty |
| 2 | 998 | 0.82 | 0.84 | 134 | empty |
| 3 | 1198 | 0.81 | 0.82 | 85 | empty |
| 4 | 747 | 0.81 | 0.84 | 93 | empty |
| 5 | 843 | 0.78 | 0.82 | 93 | JJ5, CIT |
Interfaces
6 interfaces between chains.
- C–D · 3423 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3283 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1342 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1109 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6QU3 · 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 B 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 6QU3 · PDBe 6QU3 · UniProt O15648
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