Research workbench
Structure of human short-branched chain acyl-CoA dehydrogenase (acadsb)
Analyse Structure of human short-branched chain acyl-CoA dehydrogenase (acadsb) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JIF
- Type
- protein
- Length
- 1,516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SHORT/BRANCHED chain specific acyl-CoA dehydrogenase
- EC
- 1.3.99.-
- UniProt
- P45954
- Ligands
- FAD, COS, CL
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | SHORT/BRANCHED chain specific acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 381 | 59% helix, 16% strand | P45954 |
| B, C | SHORT/BRANCHED chain specific acyl-CoA dehydrogenase (EC 1.3.99.-) | protein | 377 | 60% helix, 16% strand | P45954 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- COS · Coenzyme A persulfide · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 10 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.87 | 0.88 | 146 | FAD |
| 2 | 602 | 0.83 | 0.88 | 65 | FAD, COS |
| 3 | 681 | 0.81 | 0.85 | 78 | FAD, COS |
| 4 | 648 | 0.81 | 0.86 | 74 | FAD, COS, EDO |
| 5 | 334 | 0.58 | 0.76 | 47 | EDO |
Interfaces
6 interfaces between chains.
- B–D · 1814 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1808 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1759 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1756 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 183 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2JIF · Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB) · the same entry in another collection · chain D against D, TM-score 1.00
- P45954 · AlphaFold monomer V2.0 prediction for SHORT/BRANCHED chain specific acyl-CoA… · a predicted model of the same protein · chain D 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 P45954
- Elsewhere: RCSB PDB 2JIF · PDBe 2JIF · UniProt P45954
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