MolNFT v1 · #87049 · protein
Crystal structure of plasmodium falciparum spermidine synthase in complex with decarboxylated S-ADENOSYLMETHIONINE5' and 4- methylaniline
4BP3: “Crystal structure of plasmodium falciparum spermidine synthase in complex with decarboxylated…”. X-ray diffraction, 3 ligands (4MN, S4M, 1PG), 10 pockets (best druggability 0.83). MolNFT v1 #87049 on GenesisL1: 3D structure, binding…
- PDB
- 4BP3
- 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
- 4MN, S4M, 1PG
- Pockets
- 10 · 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 | 33% helix, 30% strand | Q8II73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 30% helix, 31% strand | Q8II73 |
Ligands and binding sites
- 4MN · 4-methylaniline · ligand · 3 copies · chains A, B, C
- 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 B, C
- GOL · Glycerol · additive · chains 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 | 164 | 0.83 | 0.98 | 28 | 1PG |
| 2 | 132 | 0.79 | 0.97 | 39 | 4MN, S4M |
| 3 | 134 | 0.79 | 0.96 | 39 | 4MN, S4M |
| 4 | 126 | 0.78 | 0.96 | 41 | 4MN, S4M |
| 5 | 254 | 0.55 | 0.77 | 27 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1502 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4BP3 · Crystal Structure of Plasmodium Falciparum Spermidine Synthase 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 4BP3 · PDBe 4BP3 · UniProt Q8II73
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