Research workbench
Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from streptococcus pneumoniae bound to NADPH in open conformations
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
- 5WPJ
- Type
- protein
- Length
- 1,576 residues
- Chains
- 4
- 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
- NDP
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 369 | 47% helix, 24% strand | A0A0D6J7E8 |
| B | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 414 | 51% helix, 22% strand | A0A0D6J7E8 |
| C | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 370 | 46% helix, 24% strand | A0A0D6J7E8 |
| D | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.34) | protein | 423 | 50% helix, 21% strand | A0A0D6J7E8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.82 | 0.83 | 96 | empty |
| 2 | 485 | 0.69 | 0.80 | 47 | empty |
| 3 | 614 | 0.69 | 0.77 | 76 | NDP |
| 4 | 496 | 0.67 | 0.78 | 59 | empty |
| 5 | 400 | 0.66 | 0.79 | 44 | empty |
Interfaces
4 interfaces between chains.
- C–D · 4846 Ų buried · 99 hydrogen bonds · protein-protein
- A–B · 4714 Ų buried · 97 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WPJ · 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 5WPJ · PDBe 5WPJ · UniProt A0A0D6J7E8
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