MolNFT v1 · #111583 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2-phenyl-1,2-thiazol-3(2H)-one
4YV2 · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2-phenyl-1,2-thiazol-3(2H)-one”. X-ray diffraction, 2 ligands (S4M, 4K3), 3 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4YV2
- Type
- protein
- Length
- 551 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, 4K3
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase, putative (EC 2.5.1.16) | protein | 278 | 32% helix, 31% strand | Q4DA73 |
| B | Spermidine synthase, putative (EC 2.5.1.16) | protein | 273 | 31% helix, 32% strand | Q4DA73 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · ligand · 2 copies · chains A, B
- 4K3 · N-phenyl-3-sulfanylpropanamide · ligand · 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 | 1081 | 0.83 | 0.84 | 126 | S4M, 4K3 |
| 2 | 53 | 0.71 | 0.98 | 16 | empty |
| 3 | 147 | 0.44 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1830 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4YV2 · Crystal structure of Trypanosoma cruzi spermidine synthase in complex with… · the same entry in another collection · chain B against B, 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 4YV2 · PDBe 4YV2 · UniProt Q4DA73
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