MolNFT v1 · #27631 · protein
Crystal structure of staphylococcus aureus hmg-CoA synthase with hmg- CoA and with acetoacetyl-CoA and acetylated cysteine
1XPK · 3-hydroxy-3-methylglutaryl CoA synthase: “Crystal structure of staphylococcus aureus hmg-CoA synthase with hmg- CoA and with acetoacetyl-CoA and…”. X-ray diffraction, 3 ligands (HMG, CAA, SO4), 14 pockets (best druggability 0.80).…
- PDB
- 1XPK
- Type
- protein
- Length
- 1,548 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
- HMG, CAA, SO4
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% 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 | 387 | 40% helix, 25% strand | Q79ZY6 |
Ligands and binding sites
- HMG · 3-hydroxy-3-methylglutaryl-coenzyme A · ligand · 3 copies · chains A, C, D
- CAA · Acetoacetyl-coenzyme A · ligand · 3 copies · chains A, B, 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.80 | 0.84 | 79 | empty |
| 2 | 705 | 0.80 | 0.84 | 81 | empty |
| 3 | 161 | 0.65 | 0.86 | 30 | HMG |
| 4 | 150 | 0.63 | 0.84 | 24 | HMG, CAA |
| 5 | 136 | 0.60 | 0.84 | 23 | CAA |
Interfaces
2 interfaces between chains.
- C–D · 2634 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2610 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 covalent (acetylation, covalent ligand).
Compared structures
- 1XPK · CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-CoA AND WITH… · 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 1XPK · PDBe 1XPK · UniProt Q79ZY6
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