MolNFT v1 · #115570 · protein
X-ray crystal structure of spermidine N1-acetyltransferase from vibrio cholerae.
5CNP · Spermidine N(1)-acetyltransferase: “X-ray crystal structure of spermidine N1-acetyltransferase from vibrio cholerae.”. X-ray diffraction, 1 ligand (MG), 15 pockets (best druggability 0.76). MolNFT v1 #115570 on GenesisL1: 3D…
- PDB
- 5CNP
- Type
- protein
- Length
- 1,025 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N(1)-acetyltransferase
- EC
- 2.3.1.57
- UniProt
- Q9KL03
- Ligands
- MG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 170 | 33% helix, 37% strand | Q9KL03 |
| B | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 171 | 30% helix, 38% strand | Q9KL03 |
| C | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 171 | 32% helix, 38% strand | Q9KL03 |
| D | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 175 | 33% helix, 37% strand | Q9KL03 |
| E, F | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 169 | 31% helix, 38% strand | Q9KL03 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, D, F
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.76 | 0.98 | 17 | empty |
| 2 | 72 | 0.74 | 0.98 | 16 | empty |
| 3 | 733 | 0.71 | 0.77 | 64 | empty |
| 4 | 722 | 0.70 | 0.77 | 59 | empty |
| 5 | 55 | 0.70 | 0.97 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 771 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 760 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 756 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 729 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 718 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 5CNP · X-ray crystal structure of Spermidine n1-acetyltransferase from Vibrio cholerae. · 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 C 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 5CNP · PDBe 5CNP · UniProt Q9KL03
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