MolNFT v1 · #111581 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine- 2- carboxamid
4YV0 · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with…”. X-ray diffraction, 2 ligands (S4M, 4JW), 10 pockets (best druggability 0.80). MolNFT v1 #111581 on GenesisL1: 3D…
- PDB
- 4YV0
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- 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, 4JW
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase, putative (EC 2.5.1.16) | protein | 269 | 32% helix, 32% strand | Q4DA73 |
| B, D | Spermidine synthase, putative (EC 2.5.1.16) | protein | 290 | 31% helix, 29% strand | Q4DA73 |
| C | Spermidine synthase, putative (EC 2.5.1.16) | protein | 273 | 32% helix, 32% strand | Q4DA73 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · ligand · 4 copies · chains A, B, C, D
- 4JW · (2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.80 | 0.95 | 40 | S4M |
| 2 | 226 | 0.80 | 0.93 | 49 | S4M |
| 3 | 126 | 0.80 | 0.98 | 23 | 4JW |
| 4 | 118 | 0.79 | 0.98 | 24 | 4JW |
| 5 | 70 | 0.74 | 0.98 | 26 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1817 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1798 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 322 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4YV0 · Crystal structure of Trypanosoma cruzi spermidine synthase in complex with… · the same entry in another collection · chain C against C, 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 4YV0 · PDBe 4YV0 · UniProt Q4DA73
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