Research workbench
3-hydroxy-3-methyl (hmg) coenzyme a reductase bound to R-mevalonate
Analyse 3-hydroxy-3-methyl (hmg) coenzyme a reductase bound to R-mevalonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I6Y
- Type
- protein
- Length
- 751 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme a reductase
- EC
- 1.1.1.88
- UniProt
- P13702
- Ligands
- MEV, SO4, NO2
- Pockets
- 7 · best druggability 0.67
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 1.1.1.88) | protein | 374 | 47% helix, 22% strand | P13702 |
| B | 3-hydroxy-3-methylglutaryl-coenzyme a reductase (EC 1.1.1.88) | protein | 377 | 46% helix, 21% strand | P13702 |
Ligands and binding sites
- MEV · (R)-mevalonate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- NO2 · Nitrite ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.67 | 0.79 | 55 | MEV, GOL, SO4 |
| 2 | 431 | 0.66 | 0.79 | 56 | SO4, MEV, GOL |
| 3 | 57 | 0.35 | 0.78 | 22 | empty |
| 4 | 63 | 0.34 | 0.77 | 18 | empty |
| 5 | 57 | 0.32 | 0.76 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 4914 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 4I6Y · 3-hydroxy-3-methyl (HMG) Coenzyme A Reductase bound to R-Mevalonate · the same entry in another collection · chain A against A, TM-score 1.00
- P13702 · AlphaFold monomer V2.0 prediction for 3-hydroxy-3-methylglutaryl- coenzyme a reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P13702
- Elsewhere: RCSB PDB 4I6Y · PDBe 4I6Y · UniProt P13702
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