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Pseudouridine and ADP bound structure of pseudouridine kinase (puki) from arabidopsis thaliana
Analyse Pseudouridine and ADP bound structure of pseudouridine kinase (puki) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C1Y
- Type
- protein
- Length
- 703 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pfkb-like carbohydrate kinase family protein
- UniProt
- Q94AT3
- Ligands
- FJF, ADP, NA
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pfkb-like carbohydrate kinase family protein | protein | 356 | 41% helix, 20% strand | Q94AT3 |
| B | Pfkb-like carbohydrate kinase family protein | protein | 347 | 37% helix, 22% strand | Q94AT3 |
Ligands and binding sites
- FJF · 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.79 | 0.85 | 55 | FJF, ADP |
| 2 | 549 | 0.67 | 0.77 | 53 | FJF, ADP |
| 3 | 249 | 0.55 | 0.77 | 39 | empty |
| 4 | 101 | 0.45 | 0.79 | 18 | empty |
| 5 | 79 | 0.43 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1368 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C1Y · Pseudouridine and ADP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis… · 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 7C1Y · PDBe 7C1Y · UniProt Q94AT3
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