Research workbench
Crystal structure of phosphofructokinase from staphylococcus aureus in complex with adenylylimidodiphosphate (the ATP analog) and fructose- 6-phosphate
Analyse Crystal structure of phosphofructokinase from staphylococcus aureus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XZ8
- Type
- protein
- Length
- 317 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent 6-phosphofructokinase
- EC
- 2.7.1.11
- UniProt
- Q2FXM8
- Ligands
- F6P, ANP, MG
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent 6-phosphofructokinase (EC 2.7.1.11) | protein | 317 | 46% helix, 19% strand | Q2FXM8 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.52 | 0.77 | 32 | F6P, MG, ANP |
| 2 | 51 | 0.33 | 0.78 | 13 | empty |
Compared structures
- 5XZ8 · Crystal Structure of Phosphofructokinase from Staphylococcus aureus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FXM8 · AlphaFold monomer V2.0 prediction for ATP-dependent 6-phosphofructokinase (Q2FXM8) · 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 Q2FXM8
- Elsewhere: RCSB PDB 5XZ8 · PDBe 5XZ8 · UniProt Q2FXM8
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