Research workbench
Crystal structure of an acyl-CoA dehydrogenase from brucella melitensis
Analyse Crystal structure of an acyl-CoA dehydrogenase from brucella melitensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W9U
- Type
- protein
- Length
- 1,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase | protein | 362 | 57% helix, 16% strand | — |
| B | Acyl-CoA dehydrogenase | protein | 376 | 56% helix, 15% strand | — |
| C | Acyl-CoA dehydrogenase | protein | 365 | 56% helix, 15% strand | — |
| D | Acyl-CoA dehydrogenase | protein | 375 | 56% helix, 15% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.82 | 0.83 | 121 | empty |
| 2 | 785 | 0.79 | 0.83 | 84 | empty |
| 3 | 645 | 0.78 | 0.83 | 63 | empty |
| 4 | 272 | 0.70 | 0.85 | 34 | empty |
| 5 | 332 | 0.63 | 0.79 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2375 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2372 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 918 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4W9U · Crystal Structure of an Acyl-CoA dehydrogenase from Brucella melitensis · 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
- Elsewhere: RCSB PDB 4W9U · PDBe 4W9U
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