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Crystal structure of spermidine synthase
Analyse Crystal structure of spermidine synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IY9
- Type
- protein
- Length
- 1,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- P70998
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Spermidine synthase (EC 2.5.1.16) | protein | 274 | 28% helix, 32% strand | P70998 |
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.98 | 24 | empty |
| 2 | 124 | 0.81 | 0.98 | 24 | empty |
| 3 | 310 | 0.78 | 0.89 | 20 | empty |
| 4 | 409 | 0.68 | 0.80 | 47 | empty |
| 5 | 424 | 0.67 | 0.79 | 43 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1638 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1626 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 586 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 P70998
- Elsewhere: RCSB PDB 1IY9 · PDBe 1IY9 · UniProt P70998
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