Research workbench
Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from yersinia pestis in complex with calcium ions.
Analyse Crystal structure of SPERMIDINE/SPERMINE N-acetyltransferase speg from yersinia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D72
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine N1-acetyltransferase
- UniProt
- Q0WD68
- Ligands
- CA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spermidine N1-acetyltransferase | protein | 170 | 35% helix, 39% strand | Q0WD68 |
| B | Spermidine N1-acetyltransferase | protein | 176 | 32% helix, 39% strand | Q0WD68 |
| C | Spermidine N1-acetyltransferase | protein | 177 | 31% helix, 38% strand | Q0WD68 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- MLI · Malonate ion · additive · 7 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.84 | 0.85 | 84 | PEG, MLI |
| 2 | 94 | 0.79 | 0.99 | 18 | empty |
| 3 | 626 | 0.69 | 0.77 | 51 | MLI |
| 4 | 100 | 0.48 | 0.81 | 14 | empty |
| 5 | 105 | 0.46 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1242 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 869 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6D72 · Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in… · 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 6D72 · PDBe 6D72 · UniProt Q0WD68
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