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Crystal structure of plasmodium falciparum spermidine synthase in complex with methylthioadenosin and spermidine after catalysis in crystal
Analyse Crystal 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
- 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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