MolNFT v1 · #39418 · protein
The crystal structure of spermidine synthase from P. falciparum in complex with 5'-methylthioadenosine
2HTE: “The crystal structure of spermidine synthase from P. falciparum in complex with 5'-methylthioadenosine”. X-ray diffraction, 4 ligands (MTA, 1PG, UNX), 11 pockets (best druggability 0.83). MolNFT v1 #39418 on GenesisL1: 3D structure…
- PDB
- 2HTE
- Type
- protein
- Length
- 823 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- Q8II73
- Ligands
- MTA, 1PG, UNX, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 272 | 31% helix, 31% strand | Q8II73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 270 | 31% helix, 32% strand | Q8II73 |
| C | Spermidine synthase (EC 2.5.1.16) | protein | 281 | 32% helix, 30% strand | Q8II73 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, B, C
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 13 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.83 | 0.98 | 28 | empty |
| 2 | 111 | 0.77 | 0.96 | 38 | MTA |
| 3 | 406 | 0.71 | 0.82 | 45 | MTA |
| 4 | 293 | 0.64 | 0.81 | 39 | MTA |
| 5 | 429 | 0.62 | 0.77 | 44 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1505 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2HTE · The crystal structure of spermidine synthase from p. falciparum in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8II73
- Elsewhere: RCSB PDB 2HTE · PDBe 2HTE · UniProt Q8II73
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