Research workbench
Structure of the glutaryl-coenzyme a dehydrogenase glutaryl-CoA complex
Analyse Structure of the glutaryl-coenzyme a dehydrogenase glutaryl-CoA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MPI
- Type
- protein
- Length
- 1,566 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaryl-CoA dehydrogenase
- EC
- 1.3.99.7
- UniProt
- C3UVB0
- Ligands
- FAD, GRA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 391 | 57% helix, 15% strand | C3UVB0 |
| B, D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 390 | 57% helix, 14% strand | C3UVB0 |
| C | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 395 | 56% helix, 15% strand | C3UVB0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- GRA · glutaryl-coenzyme A · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.75 | 0.82 | 58 | FAD, GRA |
| 2 | 646 | 0.75 | 0.81 | 80 | FAD, GRA |
| 3 | 510 | 0.74 | 0.82 | 55 | FAD, GRA |
| 4 | 477 | 0.73 | 0.82 | 54 | FAD, GRA |
| 5 | 172 | 0.65 | 0.85 | 22 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1980 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1962 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3MPI · Structure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complex · the same entry in another collection · chain C against C, TM-score 1.00
- C3UVB0 · AlphaFold monomer V2.0 prediction for glutaryl-CoA dehydrogenase (C3UVB0) · a predicted model of the same protein · chain D 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 C3UVB0
- Elsewhere: RCSB PDB 3MPI · PDBe 3MPI · UniProt C3UVB0
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