Research workbench
Crystal structure of human phosphofructokinase-1 in complex with ADP, northeast structural genomics consortium target HR9275
Analyse Crystal structure of human phosphofructokinase-1 in complex with ADP, northeast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XYK
- Type
- protein
- Length
- 2,972 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent 6-phosphofructokinase, platelet type
- EC
- 2.7.1.11
- UniProt
- Q01813
- Ligands
- ADP, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 737 | 40% helix, 17% strand | Q01813 |
| B | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 749 | 41% helix, 16% strand | Q01813 |
| C, D | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 743 | 41% helix, 16% strand | Q01813 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · 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 | 1003 | 0.85 | 0.86 | 120 | PO4 |
| 2 | 596 | 0.81 | 0.87 | 72 | empty |
| 3 | 487 | 0.81 | 0.88 | 60 | empty |
| 4 | 529 | 0.79 | 0.85 | 61 | empty |
| 5 | 544 | 0.79 | 0.85 | 61 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2571 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 2113 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 783 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 776 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4XYK · Crystal structure of human phosphofructokinase-1 in complex with ADP, Northeast… · 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 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 Q01813
- Elsewhere: RCSB PDB 4XYK · PDBe 4XYK · UniProt Q01813
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