Research workbench
Crystal structure of spermidine N-acetyltransferase from vibrio cholerae in complex with polyamine
Analyse Crystal structure of spermidine N-acetyltransferase from vibrio cholerae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MJ8
- Type
- protein
- Length
- 508 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- UniProt
- Q9KL03
- Ligands
- SPM
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N1-acetyltransferase | protein | 170 | 35% helix, 35% strand | Q9KL03 |
| B | Spermidine N1-acetyltransferase | protein | 168 | 35% helix, 35% strand | Q9KL03 |
| C | Spermidine N1-acetyltransferase | protein | 170 | 35% helix, 35% strand | Q9KL03 |
Ligands and binding sites
- SPM · Spermine · ligand · 4 copies · chains A, C, B
- EOH · Ethanol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.82 | 0.83 | 111 | SPM, EOH |
| 2 | 672 | 0.74 | 0.80 | 74 | SPM |
| 3 | 134 | 0.44 | 0.76 | 19 | empty |
| 4 | 87 | 0.40 | 0.77 | 11 | empty |
| 5 | 76 | 0.39 | 0.78 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1007 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 756 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4MJ8 · Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KL03 · AlphaFold monomer V2.0 prediction for spermidine N(1)-acetyltransferase (Q9KL03) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9KL03
- Elsewhere: RCSB PDB 4MJ8 · PDBe 4MJ8 · UniProt Q9KL03
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