MolNFT v1 · #108878 · protein
Ligand-free structure of human platelet phosphofructokinase in an R- state, crystal form I
4WL0 · ATP-dependent 6-phosphofructokinase, platelet type: “Ligand-free structure of human platelet phosphofructokinase in an R- state, crystal form I”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 4WL0
- Type
- protein
- Length
- 2,878 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
- PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 712 | 46% helix, 18% strand | Q01813 |
| B, D | ATP-dependent 6-phosphofructokinase, platelet type (EC 2.7.1.11) | protein | 727 | 46% helix, 18% strand | Q01813 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.84 | 0.85 | 104 | empty |
| 2 | 1079 | 0.83 | 0.84 | 102 | PO4 |
| 3 | 1093 | 0.83 | 0.84 | 113 | PO4 |
| 4 | 903 | 0.83 | 0.84 | 93 | empty |
| 5 | 1189 | 0.81 | 0.82 | 108 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2179 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2175 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 761 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 738 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4WL0 · Ligand-free structure of human platelet phosphofructokinase in an R-state, crystal form I · 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 B 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 4WL0 · PDBe 4WL0 · UniProt Q01813
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