Research workbench
Crystal structure of trypanosoma cruzi spermidine synthase in complex with 5-[(4-METHYLBENZYL)OXY]QUINAZOLINE-2,4-diamine
Analyse Crystal structure of trypanosoma cruzi spermidine synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YUZ
- Type
- protein
- Length
- 1,100 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, 4JV
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 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, 32% strand | Q4DA73 |
| B | Spermidine synthase, putative (EC 2.5.1.16) | protein | 276 | 33% helix, 30% strand | Q4DA73 |
| C | Spermidine synthase, putative (EC 2.5.1.16) | protein | 274 | 32% helix, 32% strand | Q4DA73 |
| D | Spermidine synthase, putative (EC 2.5.1.16) | protein | 277 | 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
- 4JV · 5-[(4-methylbenzyl)oxy]quinazoline-2,4-diamine · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.83 | 0.84 | 122 | S4M, 4JV |
| 2 | 888 | 0.80 | 0.82 | 97 | S4M, 4JV |
| 3 | 73 | 0.76 | 0.99 | 24 | empty |
| 4 | 1001 | 0.76 | 0.78 | 97 | empty |
| 5 | 55 | 0.70 | 0.98 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1827 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1764 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 385 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YUZ · 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 4YUZ · PDBe 4YUZ · UniProt Q4DA73
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