Research workbench
Crystal structure of arabidopsis thaliana spermidine synthase isoform 2 (ATSPDS2)
Analyse Crystal structure of arabidopsis thaliana spermidine synthase isoform 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O64
- Type
- protein
- Length
- 2,263 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase 2
- EC
- 2.5.1.16
- UniProt
- O48661
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase 2 (EC 2.5.1.16) | protein | 284 | 31% helix, 29% strand | O48661 |
| B | Spermidine synthase 2 (EC 2.5.1.16) | protein | 290 | 30% helix, 29% strand | O48661 |
| C | Spermidine synthase 2 (EC 2.5.1.16) | protein | 277 | 32% helix, 30% strand | O48661 |
| D | Spermidine synthase 2 (EC 2.5.1.16) | protein | 275 | 32% helix, 30% strand | O48661 |
| E | Spermidine synthase 2 (EC 2.5.1.16) | protein | 281 | 31% helix, 29% strand | O48661 |
| F | Spermidine synthase 2 (EC 2.5.1.16) | protein | 287 | 31% helix, 29% strand | O48661 |
| G | Spermidine synthase 2 (EC 2.5.1.16) | protein | 288 | 32% helix, 28% strand | O48661 |
| H | Spermidine synthase 2 (EC 2.5.1.16) | protein | 281 | 28% helix, 31% strand | O48661 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C, D, E, F, G
- ACT · Acetate ion · additive · 5 copies · chains A, B, E, F, G, H
- MLI · Malonate ion · additive · 4 copies · chains C, D, E, F, G, H
- FMT · Formic acid · additive · 3 copies · chains B, E, F
- EDO · 1,2-ethanediol · additive · chains E
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 | 1038 | 0.81 | 0.83 | 104 | FMT, ACT |
| 2 | 101 | 0.80 | 0.99 | 19 | MLI |
| 3 | 101 | 0.79 | 0.99 | 20 | MLI |
| 4 | 98 | 0.79 | 0.99 | 20 | ACT |
| 5 | 1136 | 0.79 | 0.81 | 108 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1785 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1771 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1700 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1582 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6O64 · Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2) · the same entry in another collection · chain H against H, TM-score 1.00
- O48661 · AlphaFold monomer V2.0 prediction for spermidine synthase 2 (O48661) · 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 O48661
- Elsewhere: RCSB PDB 6O64 · PDBe 6O64 · UniProt O48661
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