Research workbench
Structure of class II hmg-CoA reductase from delftia acidovorans with NAD bound
Analyse Structure of class II hmg-CoA reductase from delftia acidovorans with NAD bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DIO
- Type
- protein
- Length
- 1,231 residues
- Chains
- 3
- 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
- A0A291JGB7
- Ligands
- NAD, SO4
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.88) | protein | 376 | 46% helix, 22% strand | A0A291JGB7 |
| B | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.88) | protein | 427 | 49% helix, 19% strand | A0A291JGB7 |
| C | 3-hydroxy-3-methylglutaryl coenzyme a reductase (EC 1.1.1.88) | protein | 428 | 48% helix, 18% strand | A0A291JGB7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C
- CIT · Citric acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.84 | 0.85 | 93 | NAD, EDO, CIT |
| 2 | 924 | 0.78 | 0.81 | 93 | EDO |
| 3 | 414 | 0.67 | 0.80 | 51 | CIT, EDO, NAD |
| 4 | 546 | 0.65 | 0.76 | 51 | CIT, EDO |
| 5 | 374 | 0.63 | 0.78 | 44 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5490 Ų buried · 94 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6DIO · Structure of class II HMG-CoA reductase from Delftia acidovorans with NAD bound · 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 A0A291JGB7
- Elsewhere: RCSB PDB 6DIO · PDBe 6DIO · UniProt A0A291JGB7
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