Research workbench
Crystal structure of spermidine synthase in complex with transition state analogue adodato
Analyse Crystal structure of spermidine synthase in complex with transition state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQ3
- Type
- protein
- Length
- 1,167 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- Q9WZC2
- Ligands
- AAT
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 295 | 32% helix, 29% strand | Q9WZC2 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 286 | 31% helix, 30% strand | Q9WZC2 |
| C, D | Spermidine synthase (EC 2.5.1.16) | protein | 293 | 31% helix, 29% strand | Q9WZC2 |
Ligands and binding sites
- AAT · S-adenosyl-1,8-diamino-3-thiooctane · ligand · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.80 | 0.97 | 36 | AAT |
| 2 | 95 | 0.79 | 0.99 | 21 | empty |
| 3 | 88 | 0.78 | 0.99 | 20 | empty |
| 4 | 304 | 0.71 | 0.85 | 61 | AAT |
| 5 | 514 | 0.69 | 0.79 | 58 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1936 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1927 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1664 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1570 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1JQ3 · Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZC2 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (Q9WZC2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9WZC2
- Elsewhere: RCSB PDB 1JQ3 · PDBe 1JQ3 · UniProt Q9WZC2
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