Research workbench
Speg spermidine N-acetyltransferase from staphylococcus aureus in complex with spermine, crystal form II
Analyse Speg spermidine N-acetyltransferase from staphylococcus aureus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KY4
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diamine N-acetyltransferase
- UniProt
- U5NVV0
- Ligands
- SPM
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | Diamine N-acetyltransferase | protein | 166 | 34% helix, 36% strand | U5NVV0 |
Ligands and binding sites
- SPM · Spermine · ligand · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.84 | 0.85 | 152 | SPM |
| 2 | 342 | 0.75 | 0.86 | 51 | SPM |
| 3 | 275 | 0.71 | 0.85 | 44 | empty |
| 4 | 277 | 0.70 | 0.85 | 44 | empty |
| 5 | 150 | 0.48 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1045 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 21 hydrogen bonds · protein-protein
- C–A · 735 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 722 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 342 Ų buried · 4 hydrogen bonds · protein-protein
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 U5NVV0
- Elsewhere: RCSB PDB 7KY4 · PDBe 7KY4 · UniProt U5NVV0
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