MolNFT v1 · #111582 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with quinolin-8-yl piperidine-1-carboxylate
4YV1 · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with quinolin-8-yl…”. X-ray diffraction, 2 ligands (S4M, 4K2), 6 pockets (best druggability 0.86). MolNFT v1 #111582 on GenesisL1…
- PDB
- 4YV1
- Type
- protein
- Length
- 1,124 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, 4K2
- Pockets
- 6 · best druggability 0.86
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 | 273 | 32% helix, 31% strand | Q4DA73 |
| B, D | Spermidine synthase, putative (EC 2.5.1.16) | protein | 288 | 32% helix, 30% strand | Q4DA73 |
| C | Spermidine synthase, putative (EC 2.5.1.16) | protein | 275 | 32% helix, 31% 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
- 4K2 · quinolin-8-yl piperidine-1-carboxylate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.86 | 0.94 | 74 | S4M, 4K2 |
| 2 | 718 | 0.86 | 0.89 | 116 | S4M, 4K2 |
| 3 | 1004 | 0.76 | 0.78 | 97 | empty |
| 4 | 57 | 0.72 | 0.98 | 21 | empty |
| 5 | 297 | 0.66 | 0.82 | 46 | S4M |
Interfaces
3 interfaces between chains.
- C–D · 1806 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1794 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 373 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4YV1 · Crystal structure of Trypanosoma cruzi spermidine synthase in complex with quinolin-8-yl… · 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 4YV1 · PDBe 4YV1 · UniProt Q4DA73
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