Research workbench
Methylsuccinyl-CoA dehydrogenase of paracoccus denitrificans with bound flavin adenine dinucleotide
Analyse Methylsuccinyl-CoA dehydrogenase of paracoccus denitrificans with bound flavin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ES9
- Type
- protein
- Length
- 1,090 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.8.-
- UniProt
- A1B5Y0
- Ligands
- COA, FAD, SO4
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acyl-CoA dehydrogenase (EC 1.3.8.-) | protein | 545 | 60% helix, 12% strand | A1B5Y0 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.83 | 0.85 | 83 | FAD |
| 2 | 1025 | 0.83 | 0.84 | 95 | FAD |
| 3 | 181 | 0.83 | 0.98 | 56 | empty |
| 4 | 808 | 0.72 | 0.77 | 89 | empty |
| 5 | 279 | 0.64 | 0.81 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3152 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 6ES9 · Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine… · 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 A1B5Y0
- Elsewhere: RCSB PDB 6ES9 · PDBe 6ES9 · UniProt A1B5Y0
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