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Dodecameric structure of spermidine N-acetyltransferase speg from vibrio cholerae O1 biovar eltor
Analyse Dodecameric structure of spermidine N-acetyltransferase speg from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JJX
- Type
- protein
- Length
- 509 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- UniProt
- Q9KL03
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N1-acetyltransferase | protein | 172 | 32% helix, 35% strand | Q9KL03 |
| B | Spermidine N1-acetyltransferase | protein | 168 | 33% helix, 39% strand | Q9KL03 |
| C | Spermidine N1-acetyltransferase | protein | 169 | 30% helix, 38% strand | Q9KL03 |
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.84 | 0.85 | 98 | empty |
| 2 | 68 | 0.74 | 0.98 | 19 | empty |
| 3 | 606 | 0.71 | 0.79 | 49 | empty |
| 4 | 184 | 0.63 | 0.84 | 21 | empty |
| 5 | 68 | 0.50 | 0.85 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1129 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 233 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4JJX · Dodecameric structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae O1… · 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 0.93
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 4JJX · PDBe 4JJX · UniProt Q9KL03
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