Research workbench
Structure of the glutaryl-coenzyme a dehydrogenase
Analyse Structure of the glutaryl-coenzyme a dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPJ
- Type
- protein
- Length
- 2,350 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaryl-CoA dehydrogenase; Octapeptide
- EC
- 1.3.99.7
- UniProt
- C3UVB0
- Ligands
- FAD, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 389 | 56% helix, 15% strand | C3UVB0 |
| B | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 393 | 55% helix, 15% strand | C3UVB0 |
| D, F | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 390 | 56% helix, 16% strand | C3UVB0 |
| E | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 391 | 54% helix, 16% strand | C3UVB0 |
| Y | Octapeptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, D, E, G, F
- CL · Chloride ion · ion · 6 copies · chains A, B, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.86 | 0.93 | 56 | FAD |
| 2 | 489 | 0.85 | 0.92 | 64 | FAD |
| 3 | 804 | 0.84 | 0.86 | 80 | FAD |
| 4 | 811 | 0.83 | 0.85 | 80 | FAD |
| 5 | 577 | 0.73 | 0.81 | 51 | FAD |
Interfaces
9 interfaces between chains.
- F–G · 2023 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2017 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 1990 Ų buried · 21 hydrogen bonds · protein-protein
- D–G · 1976 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1961 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 C3UVB0
- Elsewhere: RCSB PDB 3MPJ · PDBe 3MPJ · UniProt C3UVB0
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