Research workbench
Crystal structure of hmg-CoA synthase from enterococcus faecalis with acetoacetyl-CoA ligand.
Analyse Crystal structure of hmg-CoA synthase from enterococcus faecalis with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YSL
- Type
- protein
- Length
- 766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hmg-CoA synthase
- EC
- 4.1.3.5
- Ligands
- COA, AAE, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hmg-CoA synthase (EC 4.1.3.5) | protein | 383 | 39% helix, 26% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · chains B
- AAE · Acetoacetic acid · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.75 | 0.84 | 48 | GOL |
| 2 | 389 | 0.73 | 0.84 | 36 | empty |
| 3 | 149 | 0.65 | 0.86 | 24 | AAE |
| 4 | 158 | 0.57 | 0.81 | 31 | empty |
| 5 | 68 | 0.43 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2933 Ų buried · 70 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, oxidation).
Compared structures
- 1YSL · Crystal structure of HMG-CoA synthase from Enterococcus faecalis with AcetoAcetyl-CoA… · 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
- Elsewhere: RCSB PDB 1YSL · PDBe 1YSL
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