Research workbench
Structure of PmHMGR bound to mevalonate, CoA and NAD.
Analyse Structure of PmHMGR bound to mevalonate, CoA and NAD. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8GDN
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.99
- Source
- Pseudomonas sp. 'mevalonii'
- Molecule
- 3-hydroxy-3-methylglutaryl-coenzyme A reductase
- EC
- 1.1.1.88
- UniProt
- P13702
- Ligands
- MEV, COA, NAD, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.99 · 2 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.88) | protein | 421 | 49% helix, 20% strand | P13702 |
| B | 3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.88) | protein | 378 | 46% helix, 22% strand | P13702 |
Ligands and binding sites
- MEV · (R)-mevalonate · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
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 | 827 | 0.82 | 0.85 | 100 | COA, MEV, NAD |
| 2 | 454 | 0.68 | 0.79 | 49 | SO4, MEV |
| 3 | 110 | 0.41 | 0.76 | 17 | empty |
| 4 | 64 | 0.41 | 0.81 | 13 | empty |
| 5 | 54 | 0.38 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 5589 Ų buried · 101 hydrogen bonds · protein-protein
Compared structures
- P13702 · AlphaFold monomer V2.0 prediction for 3-hydroxy-3-methylglutaryl- coenzyme a reductase… · a predicted model of the same protein · chain B 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 8GDN · PDBe 8GDN · UniProt P13702
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