MolNFT v1 · #158835 · protein
Crystal structure of arabidopsis thaliana spermidine synthase isoform 1 (ATSPDS1)
6O63 · Spermidine synthase 1: “Crystal structure of arabidopsis thaliana spermidine synthase isoform 1 (ATSPDS1)”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability 0.80). MolNFT v1 #158835 on GenesisL1: 3D structure…
- PDB
- 6O63
- Type
- protein
- Length
- 1,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase 1
- EC
- 2.5.1.16
- UniProt
- Q9ZUB3
- Ligands
- SO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase 1 (EC 2.5.1.16) | protein | 291 | 31% helix, 29% strand | Q9ZUB3 |
| B | Spermidine synthase 1 (EC 2.5.1.16) | protein | 286 | 30% helix, 29% strand | Q9ZUB3 |
| C | Spermidine synthase 1 (EC 2.5.1.16) | protein | 282 | 31% helix, 30% strand | Q9ZUB3 |
| D | Spermidine synthase 1 (EC 2.5.1.16) | protein | 281 | 30% helix, 30% strand | Q9ZUB3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.80 | 0.81 | 103 | empty |
| 2 | 102 | 0.80 | 0.99 | 22 | empty |
| 3 | 164 | 0.79 | 0.95 | 52 | PEG, GOL |
| 4 | 153 | 0.79 | 0.96 | 51 | PEG |
| 5 | 93 | 0.78 | 0.98 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2155 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 269 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6O63 · Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9ZUB3 · AlphaFold monomer V2.0 prediction for spermidine synthase 1 (Q9ZUB3) · a predicted model of the same protein · chain D 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 6O63 · PDBe 6O63 · UniProt Q9ZUB3
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