Research workbench
Human phosphofructokinase-1 liver type bound to activator na-11
Analyse Human phosphofructokinase-1 liver type bound to activator na-11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LW1
- Type
- protein
- Length
- 2,976 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent 6-phosphofructokinase, liver type
- EC
- 2.7.1.11
- UniProt
- P17858
- Ligands
- YG1, FBP, F6P, ADP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | ATP-dependent 6-phosphofructokinase, liver type (EC 2.7.1.11) | protein | 744 | 46% helix, 17% strand | P17858 |
Ligands and binding sites
- YG1 · N-{(11S)-2-[2-(5-hydroxypent-1-yn-1-yl)phenyl]-4H,10H-pyrazolo[5,1-c][1,4]benzoxazepin-7-yl}acetamide · ligand · 4 copies · chains A, D, E, F
- FBP · 1,6-di-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, D, E, F
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 4 copies · chains A, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, D, E, F
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 | 403 | 0.83 | 0.90 | 42 | YG1 |
| 2 | 397 | 0.82 | 0.90 | 43 | YG1 |
| 3 | 429 | 0.82 | 0.90 | 51 | YG1 |
| 4 | 419 | 0.82 | 0.90 | 45 | YG1 |
| 5 | 392 | 0.80 | 0.89 | 57 | empty |
Interfaces
4 interfaces between chains.
- E–F · 2397 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 2392 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 704 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 701 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7LW1 · Human phosphofructokinase-1 liver type bound to activator NA-11 · the same entry in another collection · chain A against A, TM-score 1.00
- P17858 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase, liver type… · a predicted model of the same protein · chain A 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 P17858
- Elsewhere: RCSB PDB 7LW1 · PDBe 7LW1 · UniProt P17858
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