Research workbench
ATP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana
Analyse ATP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C1Z
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.09617
- Source
- Arabidopsis thaliana
- Molecule
- PfkB-like carbohydrate kinase family protein
- UniProt
- Q94AT3
- Ligands
- ATP, MG, NA
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.09617 · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PfkB-like carbohydrate kinase family protein | protein | 356 | 39% helix, 20% strand | Q94AT3 |
| B | PfkB-like carbohydrate kinase family protein | protein | 355 | 39% helix, 22% strand | Q94AT3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.76 | 0.82 | 68 | MG, ATP |
| 2 | 629 | 0.68 | 0.77 | 53 | MG, ATP |
| 3 | 285 | 0.56 | 0.76 | 42 | empty |
| 4 | 226 | 0.54 | 0.77 | 35 | empty |
| 5 | 66 | 0.40 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1314 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7C1Z · ATP bound structure of pseudouridine kinase (puki) from arabidopsis thaliana · 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 Q94AT3
- Elsewhere: RCSB PDB 7C1Z · PDBe 7C1Z · UniProt Q94AT3
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