Research workbench
Crystal structure of spermidine N-acetyltransferase from escherichia COLI
Analyse Crystal structure of spermidine N-acetyltransferase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R9M
- Type
- protein
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N(1)-acetyltransferase
- EC
- 2.3.1.57
- UniProt
- P0A951
- Ligands
- MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 169 | 30% helix, 39% strand | P0A951 |
| B | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 163 | 31% helix, 42% strand | P0A951 |
| C | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 164 | 30% helix, 41% strand | P0A951 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.98 | 15 | empty |
| 2 | 64 | 0.73 | 0.98 | 15 | empty |
| 3 | 709 | 0.66 | 0.75 | 69 | empty |
| 4 | 548 | 0.62 | 0.74 | 51 | empty |
| 5 | 371 | 0.57 | 0.75 | 38 | empty |
Interfaces
2 interfaces between chains.
- B–C · 776 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 752 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4R9M · Crystal structure of spermidine N-acetyltransferase from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P0A951 · AlphaFold monomer V2.0 prediction for spermidine N(1)-acetyltransferase (P0A951) · 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 P0A951
- Elsewhere: RCSB PDB 4R9M · PDBe 4R9M · UniProt P0A951
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