MolNFT v1 · #88523 · protein
Crystal structure of plasmodium falciparum spermidine synthase in complex with methylthioadenosin and spermidine after catalysis in crystal
4CXM: “Crystal structure of plasmodium falciparum spermidine synthase in complex with methylthioadenosin and…”. X-ray diffraction, 2 ligands (MTA, SPD), 13 pockets (best druggability 0.83). MolNFT v1 #88523 on GenesisL1: 3D structure…
- PDB
- 4CXM
- 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
- MTA, SPD
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spermidine synthase (EC 2.5.1.16) | protein | 281 | 32% helix, 30% strand | Q8II73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 280 | 33% helix, 31% strand | Q8II73 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, B, C
- SPD · Spermidine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.83 | 0.98 | 30 | empty |
| 2 | 126 | 0.79 | 0.97 | 40 | MTA, SPD |
| 3 | 194 | 0.78 | 0.93 | 50 | MTA, SPD |
| 4 | 79 | 0.71 | 0.96 | 27 | MTA, SPD |
| 5 | 90 | 0.64 | 0.90 | 24 | SPD |
Interfaces
2 interfaces between chains.
- B–C · 1496 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 470 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4CXM · 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 4CXM · PDBe 4CXM · UniProt Q8II73
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