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Crystal structure of spermidine synthase from trypanosoma cruzi in complex with SAM at 2.3 a resolution
Analyse Crystal structure of spermidine synthase from trypanosoma cruzi 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
- 3BWC
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- Q4DA73
- Ligands
- SAM
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 282 | 32% helix, 29% strand | Q4DA73 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 271 | 32% helix, 31% strand | Q4DA73 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.70 | 0.83 | 50 | SAM |
| 2 | 263 | 0.66 | 0.82 | 38 | SAM |
| 3 | 160 | 0.45 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1785 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 3BWC · Crystal structure of spermidine synthase from Trypanosoma cruzi in complex with SAM at… · 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 Q4DA73
- Elsewhere: RCSB PDB 3BWC · PDBe 3BWC · UniProt Q4DA73
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