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Structure of the spermidine N1-acetyltransferase (speg) from coxiella burnetii
Analyse Structure of the spermidine N1-acetyltransferase (speg) from coxiella burnetii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TTH
- Type
- protein
- Length
- 1,951 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- EC
- 2.3.1.57
- UniProt
- Q83B40
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 162 | 28% helix, 40% strand | Q83B40 |
| B, G, J | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 164 | 26% helix, 39% strand | Q83B40 |
| C, K | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 162 | 27% helix, 40% strand | Q83B40 |
| D | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 161 | 27% helix, 40% strand | Q83B40 |
| E | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 163 | 26% helix, 39% strand | Q83B40 |
| F | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 162 | 27% helix, 40% strand | Q83B40 |
| H | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 163 | 26% helix, 39% strand | Q83B40 |
| I | Spermidine N1-acetyltransferase (EC 2.3.1.57) | protein | 162 | 27% helix, 40% strand | Q83B40 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.83 | 0.84 | 95 | empty |
| 2 | 1156 | 0.83 | 0.84 | 104 | empty |
| 3 | 1082 | 0.83 | 0.83 | 99 | empty |
| 4 | 1197 | 0.83 | 0.84 | 107 | empty |
| 5 | 958 | 0.82 | 0.84 | 93 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1143 Ų buried · 24 hydrogen bonds · protein-protein
- K–L · 1137 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1124 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 1121 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1110 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3TTH · Structure of the spermidine N1-acetyltransferase (speG) from Coxiella burnetii · 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 Q83B40
- Elsewhere: RCSB PDB 3TTH · PDBe 3TTH · UniProt Q83B40
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