MolNFT v1 · #58570 · protein
Crystal structure of spermidine synthase from plasmodium falciparum in complex with spermine
3B7P: “Crystal structure of spermidine synthase from plasmodium falciparum in complex with spermine”. X-ray diffraction, 2 ligands (MTA, SPM), 12 pockets (best druggability 0.83). MolNFT v1 #58570 on GenesisL1: 3D structure, binding sites…
- PDB
- 3B7P
- 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, SPM
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% 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 | 31% helix, 31% strand | Q8II73 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 3 copies · chains A, B, C
- SPM · Spermine · ligand · 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 | 166 | 0.83 | 0.98 | 30 | empty |
| 2 | 119 | 0.78 | 0.97 | 39 | MTA, SPM |
| 3 | 175 | 0.76 | 0.92 | 46 | MTA, SPM |
| 4 | 205 | 0.76 | 0.91 | 51 | MTA, SPM |
| 5 | 270 | 0.58 | 0.78 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1504 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3B7P · Crystal structure of spermidine synthase from Plasmodium falciparum 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 3B7P · PDBe 3B7P · UniProt Q8II73
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