MolNFT v1 · #111576 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with decarboxylated S-adenosylmethionine
4YUV · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with decarboxylated S-adenosylmethionine”. X-ray diffraction, 1 ligand (S4M), 4 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 4YUV
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase, putative
- EC
- 2.5.1.16
- UniProt
- Q4DA73
- Ligands
- S4M
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase, putative (EC 2.5.1.16) | protein | 285 | 33% helix, 30% strand | Q4DA73 |
| B | Spermidine synthase, putative (EC 2.5.1.16) | protein | 294 | 32% helix, 29% strand | Q4DA73 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.78 | 0.96 | 39 | S4M |
| 2 | 323 | 0.77 | 0.88 | 62 | S4M |
| 3 | 64 | 0.72 | 0.98 | 21 | empty |
| 4 | 111 | 0.38 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1877 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4YUV · Crystal structure of Trypanosoma cruzi spermidine synthase in complex with decarboxylated… · 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 4YUV · PDBe 4YUV · UniProt Q4DA73
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