MolNFT v1 · #138413 · protein
Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from yersinia pestis
5WIF · Spermidine N1-acetyltransferase: “Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from yersinia pestis”. X-ray diffraction, 2 ligands (K, BO3), 7 pockets (best druggability 0.84). MolNFT v1 #138413 on GenesisL1: 3D…
- PDB
- 5WIF
- Type
- protein
- Length
- 513 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- UniProt
- Q0WD68
- Ligands
- K, BO3
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N1-acetyltransferase | protein | 166 | 33% helix, 41% strand | Q0WD68 |
| B | Spermidine N1-acetyltransferase | protein | 173 | 32% helix, 39% strand | Q0WD68 |
| C | Spermidine N1-acetyltransferase | protein | 174 | 30% helix, 39% strand | Q0WD68 |
Ligands and binding sites
- K · Potassium ion · metal · chains C
- BO3 · Boric acid · ion · chains C
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.84 | 0.85 | 96 | empty |
| 2 | 76 | 0.74 | 0.98 | 17 | empty |
| 3 | 586 | 0.67 | 0.76 | 47 | BO3 |
| 4 | 117 | 0.48 | 0.79 | 16 | empty |
| 5 | 97 | 0.48 | 0.81 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1209 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5WIF · Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis · 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 Q0WD68
- Elsewhere: RCSB PDB 5WIF · PDBe 5WIF · UniProt Q0WD68
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