Research workbench
Crystal structure of D383A mutant from Arabidopsis thaliana complexed with Galactinol.
Analyse Crystal structure of D383A mutant from Arabidopsis thaliana complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EXH
- Type
- protein
- Length
- 1,434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Arabidopsis thaliana
- Molecule
- Probable galactinol--sucrose galactosyltransferase 6
- EC
- 2.4.1.82
- UniProt
- Q8RX87
- Ligands
- BQZ
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.63 · 1 distinct chain · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Probable galactinol--sucrose galactosyltransferase 6 (EC 2.4.1.82) | protein | 717 | 23% helix, 36% strand | Q8RX87 |
Ligands and binding sites
- BQZ · galactinol · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.71 | 0.77 | 62 | empty |
| 2 | 73 | 0.70 | 0.96 | 25 | empty |
| 3 | 275 | 0.57 | 0.77 | 31 | BQZ |
| 4 | 277 | 0.56 | 0.76 | 35 | BQZ |
| 5 | 230 | 0.53 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- B–A · 1324 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- Q8RX87 · AlphaFold monomer V2.0 prediction for probable galactinol--sucrose galactosyltransferase… · 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 Q8RX87
- Elsewhere: RCSB PDB 7EXH · PDBe 7EXH · UniProt Q8RX87
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