MolNFT v1 · #48433 · protein
The structure of plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine
2PT6: “The structure of plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine”. X-ray diffraction, 2 ligands (S4M, 1PG), 12 pockets (best druggability 0.83). MolNFT v1 #48433 on GenesisL1: 3D…
- PDB
- 2PT6
- Type
- protein
- Length
- 842 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
- S4M, 1PG
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spermidine synthase (EC 2.5.1.16) | protein | 281 | 31% helix, 30% strand | Q8II73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 34% helix, 31% strand | Q8II73 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · 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
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.83 | 0.98 | 28 | empty |
| 2 | 295 | 0.81 | 0.92 | 52 | S4M |
| 3 | 149 | 0.80 | 0.96 | 43 | S4M |
| 4 | 132 | 0.78 | 0.96 | 39 | S4M |
| 5 | 260 | 0.57 | 0.77 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1502 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 488 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2PT6 · The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated… · 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 2PT6 · PDBe 2PT6 · UniProt Q8II73
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