Research workbench
ATP-bound structure of human platelet phosphofructokinase in an R-state, crystal form II
Analyse ATP-bound structure of human platelet phosphofructokinase in an R-state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U1R
- Type
- protein
- Length
- 2,929 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- ATP-dependent 6-phosphofructokinase, platelet type
- EC
- 2.7.1.11
- UniProt
- Q01813
- Ligands
- ATP, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 733 | 46% helix, 19% strand | Q01813 |
| B, C | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 732 | 47% helix, 18% strand | Q01813 |
| D | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 732 | 47% helix, 18% strand | Q01813 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 12 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.83 | 0.84 | 86 | empty |
| 2 | 664 | 0.81 | 0.86 | 69 | empty |
| 3 | 663 | 0.80 | 0.84 | 59 | empty |
| 4 | 696 | 0.80 | 0.84 | 58 | empty |
| 5 | 668 | 0.79 | 0.84 | 61 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2448 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2404 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 778 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 775 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4U1R · ATP-bound structure of human platelet phosphofructokinase in an R- state, crystal form II · the same entry in another collection · chain A against A, TM-score 1.00
- Q01813 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase, platelet type… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q01813
- Elsewhere: RCSB PDB 4U1R · PDBe 4U1R · UniProt Q01813
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