MolNFT v1 · #59719 · protein
Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine
3C6K: “Crystal structure of human spermine synthase in complex with spermidine and 5-methylthioadenosine”. X-ray diffraction, 2 ligands (MTA, SPD), 18 pockets (best druggability 0.75). MolNFT v1 #59719 on GenesisL1: 3D structure, binding…
- PDB
- 3C6K
- Type
- protein
- Length
- 1,374 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermine synthase
- EC
- 2.5.1.22
- UniProt
- P52788
- Ligands
- MTA, SPD
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermine synthase (EC 2.5.1.22) | protein | 335 | 27% helix, 38% strand | P52788 |
| B | Spermine synthase (EC 2.5.1.22) | protein | 345 | 27% helix, 36% strand | P52788 |
| C | Spermine synthase (EC 2.5.1.22) | protein | 346 | 27% helix, 37% strand | P52788 |
| D | Spermine synthase (EC 2.5.1.22) | protein | 348 | 28% helix, 36% strand | P52788 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- SPD · Spermidine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.75 | 0.97 | 28 | MTA |
| 2 | 324 | 0.74 | 0.86 | 57 | MTA, SPD |
| 3 | 75 | 0.73 | 0.97 | 26 | MTA |
| 4 | 79 | 0.73 | 0.96 | 27 | MTA |
| 5 | 52 | 0.70 | 0.98 | 20 | empty |
Interfaces
2 interfaces between chains.
- C–D · 2426 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2365 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3C6K · Crystal structure of human spermine synthase in complex with spermidine and… · the same entry in another collection · chain D against D, TM-score 1.00
- P52788 · AlphaFold monomer V2.0 prediction for spermine synthase (P52788) · a predicted model of the same protein · 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 P52788
- Elsewhere: RCSB PDB 3C6K · PDBe 3C6K · UniProt P52788
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