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Spermine/spermidine N1-acetyltransferase from mouse: Crystal structure of a ternary complex reveals solvent-mediated spermine binding
Analyse Spermine/spermidine N1-acetyltransferase from mouse: Crystal structure of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BJ8
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Mus musculus
- Molecule
- Diamine acetyltransferase 1
- EC
- 2.3.1.57
- UniProt
- P48026
- Ligands
- COA, SPM
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diamine acetyltransferase 1 (EC 2.3.1.57) | protein | 163 | 39% helix, 30% strand | P48026 |
| B | Diamine acetyltransferase 1 (EC 2.3.1.57) | protein | 162 | 38% helix, 30% strand | P48026 |
| C | Diamine acetyltransferase 1 (EC 2.3.1.57) | protein | 158 | 41% helix, 31% strand | P48026 |
| D | Diamine acetyltransferase 1 (EC 2.3.1.57) | protein | 161 | 39% helix, 30% strand | P48026 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.79 | 0.80 | 83 | SPM, COA |
| 2 | 1045 | 0.79 | 0.80 | 86 | COA |
| 3 | 143 | 0.56 | 0.82 | 16 | empty |
| 4 | 86 | 0.53 | 0.84 | 16 | empty |
| 5 | 171 | 0.45 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3547 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3429 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 123 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 113 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BJ8 · SPERMINE/SPERMIDINE N1-acetyltransferase from mouse: crystal structure of a ternary… · the same entry in another collection · chain D against D, TM-score 1.00
- P48026 · AlphaFold monomer V2.0 prediction for diamine acetyltransferase 1 (P48026) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P48026
- Elsewhere: RCSB PDB 3BJ8 · PDBe 3BJ8 · UniProt P48026
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