Research workbench
Crystal structure of fructokinase with bound ATP from xylella fastidiosa
Analyse Crystal structure of fructokinase with bound ATP from xylella fastidiosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LKI
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructokinase
- EC
- 2.7.1.4
- UniProt
- Q87CC0
- Ligands
- ATP, K, PO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructokinase (EC 2.7.1.4) | protein | 313 | 45% helix, 22% strand | Q87CC0 |
| B | Fructokinase (EC 2.7.1.4) | protein | 322 | 44% helix, 22% strand | Q87CC0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.71 | 0.80 | 59 | PO4, ATP |
| 2 | 154 | 0.49 | 0.78 | 28 | empty |
| 3 | 129 | 0.45 | 0.77 | 19 | empty |
| 4 | 65 | 0.36 | 0.78 | 18 | empty |
| 5 | 110 | 0.35 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 3LKI · Crystal Structure of Fructokinase with bound ATP from Xylella fastidiosa · the same entry in another collection · 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 Q87CC0
- Elsewhere: RCSB PDB 3LKI · PDBe 3LKI · UniProt Q87CC0
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