MolNFT v1 · #180339 · protein
Spermidine N-acetyltransferase speg K23-Y30 chimera from vibrio cholerae and hssat
7KWH · Spermidine N(1)-acetyltransferase: “Spermidine N-acetyltransferase speg K23-Y30 chimera from vibrio cholerae and hssat”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.86). MolNFT v1 #180339 on GenesisL1: 3D…
- PDB
- 7KWH
- Type
- protein
- Length
- 1,999 residues
- Chains
- 12
- 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
- PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, K | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 168 | 33% helix, 36% strand | Q9KL03 |
| C | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 167 | 31% helix, 38% strand | Q9KL03 |
| D | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 164 | 29% helix, 37% strand | Q9KL03 |
| F, J, L, G, H, I | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 166 | 33% helix, 37% strand | Q9KL03 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, F, J, K, H
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 | 906 | 0.86 | 0.87 | 106 | empty |
| 2 | 862 | 0.85 | 0.87 | 91 | empty |
| 3 | 628 | 0.84 | 0.89 | 89 | empty |
| 4 | 500 | 0.83 | 0.90 | 67 | empty |
| 5 | 482 | 0.82 | 0.89 | 60 | empty |
Interfaces
24 interfaces between chains.
- K–I · 1206 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1187 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1182 Ų buried · 18 hydrogen bonds · protein-protein
- J–L · 1176 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1161 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7KWH · Spermidine N-acetyltransferase SpeG K23-Y30 chimera from Vibrio cholerae and hSSAT · the same entry in another collection · chain I against I, 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 Q9KL03
- Elsewhere: RCSB PDB 7KWH · PDBe 7KWH · UniProt Q9KL03
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