Research workbench
Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from streptococcus pneumoniae bound to hmg-CoA and in a partially closed conformation
Analyse Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WPK
- Type
- protein
- Length
- 803 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl coenzyme a reductase
- EC
- 1.1.1.34
- UniProt
- A0A0D6J7E8
- Ligands
- HMG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 381 | 46% helix, 24% strand | A0A0D6J7E8 |
| B | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 422 | 49% helix, 21% strand | A0A0D6J7E8 |
Ligands and binding sites
- HMG · 3-hydroxy-3-methylglutaryl-coenzyme A · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.80 | 0.82 | 101 | GOL, HMG |
| 2 | 751 | 0.79 | 0.83 | 64 | HMG |
| 3 | 62 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4644 Ų buried · 100 hydrogen bonds · protein-protein
Compared structures
- 5WPK · Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus… · 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 A0A0D6J7E8
- Elsewhere: RCSB PDB 5WPK · PDBe 5WPK · UniProt A0A0D6J7E8
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