MolNFT v1 · #73520 · protein
Crystal structure of spermidine synthase from E. COLI
3O4F: “Crystal structure of spermidine synthase from E. COLI”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.77). MolNFT v1 #73520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3O4F
- Type
- protein
- Length
- 2,207 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- P09158
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 282 | 30% helix, 29% strand | P09158 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 270 | 32% helix, 32% strand | P09158 |
| C | Spermidine synthase (EC 2.5.1.16) | protein | 284 | 30% helix, 29% strand | P09158 |
| D | Spermidine synthase (EC 2.5.1.16) | protein | 276 | 32% helix, 32% strand | P09158 |
| E | Spermidine synthase (EC 2.5.1.16) | protein | 283 | 31% helix, 29% strand | P09158 |
| F | Spermidine synthase (EC 2.5.1.16) | protein | 269 | 30% helix, 30% strand | P09158 |
| G | Spermidine synthase (EC 2.5.1.16) | protein | 279 | 30% helix, 29% strand | P09158 |
| H | Spermidine synthase (EC 2.5.1.16) | protein | 264 | 33% helix, 30% strand | P09158 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 31 copies · chains A, B, E, C, G, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.77 | 0.81 | 84 | SO4 |
| 2 | 740 | 0.76 | 0.81 | 72 | SO4 |
| 3 | 75 | 0.75 | 0.98 | 20 | empty |
| 4 | 68 | 0.74 | 0.98 | 21 | empty |
| 5 | 71 | 0.74 | 0.98 | 21 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1756 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1727 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1694 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 956 Ų buried · 11 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 P09158
- Elsewhere: RCSB PDB 3O4F · PDBe 3O4F · UniProt P09158
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