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Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae in complex with manganese ions.
Analyse Crystal structure of spermidine/spermine 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
- 6CX8
- Type
- protein
- Length
- 1,020 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.41
- Source
- Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
- Molecule
- Spermidine N(1)-acetyltransferase
- EC
- 2.3.1.57
- UniProt
- Q9KL03
- Ligands
- MN, PO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.41 · 4 distinct chains · 33% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 173 | 33% helix, 38% strand | Q9KL03 |
| B | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 170 | 33% helix, 38% strand | Q9KL03 |
| C, D, F | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 169 | 33% helix, 38% strand | Q9KL03 |
| E | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 170 | 34% helix, 38% strand | Q9KL03 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, D, E
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B, C, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.86 | 0.88 | 109 | empty |
| 2 | 866 | 0.86 | 0.88 | 92 | MPD |
| 3 | 774 | 0.85 | 0.88 | 93 | IPA |
| 4 | 97 | 0.77 | 0.98 | 17 | empty |
| 5 | 94 | 0.77 | 0.98 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1193 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1188 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1175 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 795 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 771 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6CX8 · Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from vibrio cholerae in… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9KL03 · AlphaFold monomer V2.0 prediction for spermidine N(1)-acetyltransferase (Q9KL03) · a predicted model of the same protein · chain D 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 6CX8 · PDBe 6CX8 · UniProt Q9KL03
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