MolNFT v1 · #27632 · protein
Crystal structure of staphylococcus aureus hmg-CoA synthase with acetoacetyl-CoA and acetylated cysteine
1XPL · 3-hydroxy-3-methylglutaryl CoA synthase: “Crystal structure of staphylococcus aureus hmg-CoA synthase with acetoacetyl-CoA and acetylated cysteine”. X-ray diffraction, 2 ligands (CAA, SO4), 11 pockets (best druggability 0.82).…
- PDB
- 1XPL
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl CoA synthase
- EC
- 2.3.3.10
- UniProt
- Q79ZY6
- Ligands
- CAA, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxy-3-methylglutaryl CoA synthase (EC 2.3.3.10) | protein | 389 | 41% helix, 25% strand | Q79ZY6 |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.82 | 0.85 | 103 | empty |
| 2 | 747 | 0.81 | 0.84 | 84 | empty |
| 3 | 768 | 0.80 | 0.84 | 83 | empty |
| 4 | 154 | 0.63 | 0.84 | 23 | CAA |
| 5 | 155 | 0.61 | 0.84 | 20 | CAA |
Interfaces
5 interfaces between chains.
- A–B · 2600 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2592 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 226 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 1XPL · Crystal Structure of Staphylococcus aureus HMG-COA Synthase with Acetoacetyl-COA and… · 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 Q79ZY6
- Elsewhere: RCSB PDB 1XPL · PDBe 1XPL · UniProt Q79ZY6
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