Research workbench
The structure of plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4- methylcyclohexylamine (4MCHA)
Analyse The structure of plasmodium falciparum spermidine synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PT9
- Type
- protein
- Length
- 841 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, 2MH, 1PG, SO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 281 | 31% helix, 30% strand | Q8II73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 32% helix, 30% strand | Q8II73 |
| C | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 32% 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
- 2MH · cis-4-methylcyclohexanamine · 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
- SO4 · Sulfate ion · ion · chains B
- 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.84 | 0.95 | 50 | S4M, 2MH |
| 2 | 177 | 0.83 | 0.97 | 30 | empty |
| 3 | 173 | 0.81 | 0.96 | 38 | S4M, 2MH |
| 4 | 163 | 0.81 | 0.96 | 38 | S4M, 2MH |
| 5 | 460 | 0.62 | 0.76 | 47 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1509 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 483 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2PT9 · 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 2PT9 · PDBe 2PT9 · UniProt Q8II73
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