MolNFT v1 · #158837 · protein
Crystal structure of arabidopsis thaliana spermidine synthase isoform 1 (ATSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine
6O65 · Spermidine synthase 1: “Crystal structure of arabidopsis thaliana spermidine synthase isoform 1 (ATSPDS1) in complex with…”. X-ray diffraction, 3 ligands (S4M, HAI, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #158837 on…
- PDB
- 6O65
- Type
- protein
- Length
- 2,333 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase 1
- EC
- 2.5.1.16
- UniProt
- Q9ZUB3
- Ligands
- S4M, HAI, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Spermidine synthase 1 (EC 2.5.1.16) | protein | 289 | 31% helix, 29% strand | Q9ZUB3 |
| B, H | Spermidine synthase 1 (EC 2.5.1.16) | protein | 294 | 29% helix, 29% strand | Q9ZUB3 |
| C | Spermidine synthase 1 (EC 2.5.1.16) | protein | 291 | 29% helix, 29% strand | Q9ZUB3 |
| D, F | Spermidine synthase 1 (EC 2.5.1.16) | protein | 293 | 30% helix, 29% strand | Q9ZUB3 |
| E | Spermidine synthase 1 (EC 2.5.1.16) | protein | 290 | 30% helix, 29% strand | Q9ZUB3 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- HAI · Cyclohexylammonium ion · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, E, G
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains E, G
- EDO · 1,2-ethanediol · additive · 2 copies · chains F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.81 | 0.97 | 47 | S4M, HAI |
| 2 | 170 | 0.81 | 0.96 | 47 | S4M, HAI |
| 3 | 162 | 0.81 | 0.96 | 46 | S4M, HAI |
| 4 | 147 | 0.80 | 0.96 | 40 | S4M, HAI |
| 5 | 147 | 0.80 | 0.96 | 39 | S4M, HAI |
Interfaces
10 interfaces between chains.
- A–B · 1785 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1775 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1775 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 1759 Ų buried · 34 hydrogen bonds · protein-protein
- F–G · 492 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6O65 · Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9ZUB3 · AlphaFold monomer V2.0 prediction for spermidine synthase 1 (Q9ZUB3) · a predicted model of the same protein · chain E 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 6O65 · PDBe 6O65 · UniProt Q9ZUB3
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