MolNFT v1 · #114091 · protein
Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2-(2-FLUOROPHENYL)ETHANAMINE
5B1S · Spermidine synthase, putative: “Crystal structure of trypanosoma cruzi spermidine synthase in complex with 2-(2-FLUOROPHENYL)ETHANAMINE”. X-ray diffraction, 2 ligands (S4M, BSX), 9 pockets (best druggability 0.80). MolNFT v1 #114091…
- PDB
- 5B1S
- Type
- protein
- Length
- 1,176 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, BSX
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Spermidine synthase, putative (EC 2.5.1.16) | protein | 294 | 32% helix, 29% 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
- BSX · 2-(2-fluorophenyl)ethanamine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.97 | 40 | S4M, BSX |
| 2 | 1070 | 0.79 | 0.81 | 93 | empty |
| 3 | 138 | 0.79 | 0.96 | 40 | S4M, BSX |
| 4 | 137 | 0.79 | 0.96 | 40 | S4M, BSX |
| 5 | 127 | 0.78 | 0.96 | 38 | S4M, BSX |
Interfaces
5 interfaces between chains.
- A–B · 1870 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1829 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 293 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 241 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 99 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5B1S · 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 5B1S · PDBe 5B1S · UniProt Q4DA73
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