Research workbench
Crystal structure of speg allosteric polyamine acetyltransferase from bacillus thuringiensis in complex with spermine
Analyse Crystal structure of speg allosteric polyamine acetyltransferase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VFN
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- EC
- 2.3.1.57, 6.3.5.2
- UniProt
- A0A0G3E2X5
- Ligands
- SPM
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Spermidine N1-acetyltransferase (EC 2.3.1.57, 6.3.5.2) | protein | 167 | 37% helix, 35% strand | A0A0G3E2X5 |
Ligands and binding sites
- SPM · Spermine · ligand · 12 copies · chains A, F, B, C, D, E, H, I, J, G, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.83 | 0.85 | 118 | SPM |
| 2 | 598 | 0.78 | 0.84 | 85 | SPM |
| 3 | 538 | 0.77 | 0.84 | 69 | SPM |
| 4 | 248 | 0.70 | 0.85 | 46 | SPM |
| 5 | 229 | 0.69 | 0.85 | 43 | SPM |
Interfaces
24 interfaces between chains.
- F–K · 991 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 990 Ų buried · 27 hydrogen bonds · protein-protein
- J–L · 989 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 981 Ų buried · 20 hydrogen bonds · protein-protein
- B–I · 974 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6VFN · Crystal structure of SpeG allosteric polyamine acetyltransferase from Bacillus… · the same entry in another collection · 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 A0A0G3E2X5
- Elsewhere: RCSB PDB 6VFN · PDBe 6VFN · UniProt A0A0G3E2X5
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