MolNFT v1 · #111578 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2H-1,4-benzothiazin-3-amine
4YUX · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2H-1,4-benzothiazin-3-amine”. X-ray diffraction, 2 ligands (S4M, 4JT), 5 pockets (best druggability 0.80). MolNFT v1 #111578…
- PDB
- 4YUX
- Type
- protein
- Length
- 587 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, 4JT
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase, putative (EC 2.5.1.16) | protein | 293 | 33% helix, 29% 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
- 4JT · 2H-1,4-benzothiazin-3-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.80 | 0.96 | 38 | S4M, 4JT |
| 2 | 102 | 0.76 | 0.97 | 29 | 4JT |
| 3 | 54 | 0.71 | 0.98 | 17 | empty |
| 4 | 75 | 0.70 | 0.95 | 22 | S4M |
| 5 | 148 | 0.42 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4YUX · Crystal structure of Trypanosoma cruzi 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 Q4DA73
- Elsewhere: RCSB PDB 4YUX · PDBe 4YUX · UniProt Q4DA73
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.