MolNFT v1 · #46306 · protein
Human spermidine synthase
2O0L: “Human spermidine synthase”. X-ray diffraction, 1 ligand (S4M), 7 pockets (best druggability 0.79). MolNFT v1 #46306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2O0L
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- P19623
- Ligands
- S4M
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine synthase (EC 2.5.1.16) | protein | 274 | 32% helix, 32% strand | P19623 |
| B | Spermidine synthase (EC 2.5.1.16) | protein | 285 | 33% helix, 31% strand | P19623 |
Ligands and binding sites
- S4M · 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.79 | 0.93 | 47 | S4M |
| 2 | 69 | 0.74 | 0.99 | 25 | empty |
| 3 | 57 | 0.73 | 0.99 | 22 | empty |
| 4 | 439 | 0.68 | 0.80 | 50 | S4M |
| 5 | 74 | 0.55 | 0.86 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1759 Ų buried · 26 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 P19623
- Elsewhere: RCSB PDB 2O0L · PDBe 2O0L · UniProt P19623
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