MolNFT v1 · #35253 · protein
Crystal structure of spermidine synthase from pyrococcus horikoshii OT3
2E5W · Probable spermidine synthase: “Crystal structure of spermidine synthase from pyrococcus horikoshii OT3”. X-ray diffraction, 2 ligands (AG3, MTA), 7 pockets (best druggability 0.81). MolNFT v1 #35253 on GenesisL1: 3D structure…
- PDB
- 2E5W
- Type
- protein
- Length
- 1,098 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable spermidine synthase
- EC
- 2.5.1.16
- UniProt
- O57950
- Ligands
- AG3, MTA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Probable spermidine synthase (EC 2.5.1.16) | protein | 280 | 31% helix, 33% strand | O57950 |
| B, D | Probable spermidine synthase (EC 2.5.1.16) | protein | 269 | 32% helix, 33% strand | O57950 |
Ligands and binding sites
- AG3 · 1-{4-[(3-aminopropyl)amino]butyl}guanidine · ligand · 2 copies · chains A, C
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.81 | 0.82 | 86 | ACT |
| 2 | 118 | 0.77 | 0.96 | 34 | AG3, MTA |
| 3 | 116 | 0.75 | 0.95 | 34 | AG3, MTA |
| 4 | 497 | 0.75 | 0.83 | 51 | empty |
| 5 | 537 | 0.73 | 0.81 | 49 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1885 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1855 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 398 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 179 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2E5W · Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
- O57950 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (O57950) · 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 O57950
- Elsewhere: RCSB PDB 2E5W · PDBe 2E5W · UniProt O57950
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