MolNFT v1 · #39859 · protein
The crystal structure of spermidine synthase from P. falciparum in complex with adodato
2I7C: “The crystal structure of spermidine synthase from P. falciparum in complex with adodato”. X-ray diffraction, 2 ligands (AAT, 1PG), 12 pockets (best druggability 0.82). MolNFT v1 #39859 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2I7C
- 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
- AAT, 1PG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 32% helix, 31% strand | Q8II73 |
Ligands and binding sites
- AAT · S-adenosyl-1,8-diamino-3-thiooctane · 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 | 165 | 0.82 | 0.98 | 28 | empty |
| 2 | 134 | 0.79 | 0.96 | 36 | AAT |
| 3 | 136 | 0.78 | 0.96 | 39 | AAT |
| 4 | 138 | 0.78 | 0.96 | 40 | AAT |
| 5 | 281 | 0.58 | 0.78 | 29 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1506 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 487 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2I7C · The crystal structure of spermidine synthase from p. falciparum in complex with AdoDATO · 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 2I7C · PDBe 2I7C · UniProt Q8II73
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