Research workbench
X-ray structure of spermidine synthase from arabidopsis thaliana gene AT1G23820
Analyse X-ray structure of spermidine synthase from arabidopsis thaliana gene AT1G23820 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XJ5
- Type
- protein
- Length
- 1,150 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Arabidopsis thaliana
- Molecule
- Spermidine synthase 1
- EC
- 2.5.1.16
- UniProt
- Q9ZUB3
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spermidine synthase 1 (EC 2.5.1.16) | protein | 290 | 32% helix, 29% strand | Q9ZUB3 |
| B, D | Spermidine synthase 1 (EC 2.5.1.16) | protein | 285 | 32% helix, 29% strand | Q9ZUB3 |
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.82 | 0.99 | 20 | empty |
| 2 | 112 | 0.80 | 0.98 | 20 | empty |
| 3 | 693 | 0.79 | 0.84 | 100 | empty |
| 4 | 366 | 0.75 | 0.86 | 56 | empty |
| 5 | 77 | 0.73 | 0.97 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1895 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1870 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 996 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 174 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 1XJ5 · X-ray structure of spermidine synthase from arabidopsis thaliana gene AT1G23820 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZUB3 · AlphaFold monomer V2.0 prediction for spermidine synthase 1 (Q9ZUB3) · 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 Q9ZUB3
- Elsewhere: RCSB PDB 1XJ5 · PDBe 1XJ5 · UniProt Q9ZUB3
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