Research workbench
Crystal structure of acyl-CoA dehydrogenase from burkholderia thailandensis E264
Analyse Crystal structure of acyl-CoA dehydrogenase from burkholderia thailandensis E264 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M9A
- Type
- protein
- Length
- 1,483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- EC
- 1.3.99.-
- UniProt
- Q2T4A2
- Ligands
- FDA
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 371 | 58% helix, 15% strand | Q2T4A2 |
| B | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 376 | 58% helix, 16% strand | Q2T4A2 |
| C | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 372 | 59% helix, 16% strand | Q2T4A2 |
| D | Acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 364 | 58% helix, 15% strand | Q2T4A2 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.84 | 0.88 | 60 | FDA |
| 2 | 903 | 0.81 | 0.83 | 62 | empty |
| 3 | 882 | 0.78 | 0.81 | 60 | empty |
| 4 | 738 | 0.75 | 0.80 | 53 | empty |
| 5 | 753 | 0.73 | 0.79 | 83 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1775 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1668 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1418 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1250 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 199 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4M9A · Crystal structure of Acyl-coA dehydrogenase from Burkholderia thailandensis E264 · 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 Q2T4A2
- Elsewhere: RCSB PDB 4M9A · PDBe 4M9A · UniProt Q2T4A2
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