Research workbench
Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from escherichia COLI in complex with TRIS(HYDROXYMETHYL)AMINOMETHANE.
Analyse Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CY6
- Type
- protein
- Length
- 169 residues
- Chains
- 1
- 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
- NA, CL
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N(1)-acetyltransferase (EC 2.3.1.57) | protein | 169 | 34% helix, 37% strand | P0A951 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 8 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.65 | 0.78 | 43 | CL, MRD, MPD |
| 2 | 55 | 0.44 | 0.84 | 12 | MRD |
Compared structures
- 6CY6 · Crystal structure of spermidine/spermine N-acetyltransferase SpeG 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 A against A, TM-score 0.94
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 6CY6 · PDBe 6CY6 · UniProt P0A951
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