Research workbench
Crystal structure of human spermine synthase in complex with spermine and 5-methylthioadenosine
Analyse Crystal structure of human spermine synthase in complex with spermine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C6M
- Type
- protein
- Length
- 1,247 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, SPM
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermine synthase (EC 2.5.1.22) | protein | 336 | 28% helix, 37% strand | P52788 |
| B | Spermine synthase (EC 2.5.1.22) | protein | 342 | 27% helix, 37% strand | P52788 |
| C | Spermine synthase (EC 2.5.1.22) | protein | 291 | 27% helix, 33% strand | P52788 |
| D | Spermine synthase (EC 2.5.1.22) | protein | 278 | 24% helix, 36% strand | P52788 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- SPM · Spermine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.76 | 0.88 | 54 | MTA, SPM |
| 2 | 955 | 0.76 | 0.78 | 88 | empty |
| 3 | 114 | 0.75 | 0.95 | 31 | MTA, SPM |
| 4 | 156 | 0.75 | 0.92 | 44 | MTA, SPM |
| 5 | 77 | 0.73 | 0.97 | 23 | MTA |
Interfaces
5 interfaces between chains.
- A–B · 2463 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 1873 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 353 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 32 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C6M · Crystal structure of human spermine synthase in complex with spermine 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 C 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 3C6M · PDBe 3C6M · UniProt P52788
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