MolNFT v1 · #140252 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with N-(4-METHOXYPHENYL)QUINOLIN-4-amine
5Y4Q · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with N-(4-METHOXYPHENYL)QUINOLIN-4-amine”. X-ray diffraction, 2 ligands (S4M, 8OF), 10 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5Y4Q
- Type
- protein
- Length
- 1,094 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, 8OF
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase, putative (EC 2.5.1.16) | protein | 273 | 31% helix, 31% strand | Q4DA73 |
| B | Spermidine synthase, putative (EC 2.5.1.16) | protein | 279 | 30% helix, 30% strand | Q4DA73 |
| C | Spermidine synthase, putative (EC 2.5.1.16) | protein | 272 | 31% helix, 30% strand | Q4DA73 |
| D | Spermidine synthase, putative (EC 2.5.1.16) | protein | 270 | 31% 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
- 8OF · N-(4-methoxyphenyl)quinolin-4-amine · ligand · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.81 | 0.87 | 73 | S4M, 8OF |
| 2 | 443 | 0.80 | 0.88 | 59 | S4M, 8OF |
| 3 | 408 | 0.74 | 0.84 | 60 | S4M, 8OF |
| 4 | 949 | 0.74 | 0.77 | 94 | empty |
| 5 | 306 | 0.72 | 0.85 | 53 | S4M, 8OF |
Interfaces
3 interfaces between chains.
- A–B · 1947 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1792 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y4Q · 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 5Y4Q · PDBe 5Y4Q · UniProt Q4DA73
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