MolNFT v1 · #56860 · protein
Crystal structure of spermidine synthase from pyrococcus horikoshii OT3, P1 form
2ZSU: “Crystal structure of spermidine synthase from pyrococcus horikoshii OT3, P1 form”. X-ray diffraction, 1 ligand (AG3), 14 pockets (best druggability 0.77). MolNFT v1 #56860 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ZSU
- Type
- protein
- Length
- 1,654 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- O57950
- Ligands
- AG3
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 33% helix, 33% strand | O57950 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 278 | 34% helix, 33% strand | O57950 |
| C | Spermidine synthase (EC 2.5.1.16) | protein | 273 | 33% helix, 33% strand | O57950 |
| D | Spermidine synthase (EC 2.5.1.16) | protein | 271 | 32% helix, 34% strand | O57950 |
| E | Spermidine synthase (EC 2.5.1.16) | protein | 279 | 35% helix, 33% strand | O57950 |
| F | Spermidine synthase (EC 2.5.1.16) | protein | 273 | 32% helix, 33% strand | O57950 |
Ligands and binding sites
- AG3 · 1-{4-[(3-aminopropyl)amino]butyl}guanidine · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.77 | 0.79 | 109 | empty |
| 2 | 219 | 0.72 | 0.88 | 39 | AG3 |
| 3 | 196 | 0.71 | 0.88 | 36 | AG3 |
| 4 | 232 | 0.65 | 0.83 | 38 | AG3 |
| 5 | 211 | 0.61 | 0.81 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1911 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1909 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1899 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 500 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 369 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2ZSU · Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3, P1 form · the same entry in another collection · chain F against F, TM-score 1.00
- O57950 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (O57950) · a predicted model of the same protein · chain C 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 O57950
- Elsewhere: RCSB PDB 2ZSU · PDBe 2ZSU · UniProt O57950
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