Research workbench
Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA
Analyse Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JQI
- Type
- protein
- Length
- 768 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain acyl-CoA dehydrogenase
- EC
- 1.3.99.2
- UniProt
- P15651
- Ligands
- CAA, FAD
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Short chain acyl-CoA dehydrogenase (EC 1.3.99.2) | protein | 384 | 57% helix, 15% strand | P15651 |
Ligands and binding sites
- CAA · Acetoacetyl-coenzyme A · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.81 | 0.86 | 65 | CAA, FAD |
| 2 | 592 | 0.81 | 0.86 | 66 | CAA, FAD |
| 3 | 107 | 0.55 | 0.85 | 24 | empty |
| 4 | 145 | 0.40 | 0.74 | 30 | empty |
| 5 | 75 | 0.38 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1857 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 1JQI · Crystal Structure of Rat Short Chain Acyl-CoA Dehydrogenase Complexed With Acetoacetyl-CoA · the same entry in another collection · chain A against A, TM-score 1.00
- P15651 · AlphaFold monomer V2.0 prediction for short-chain specific acyl-CoA dehydrogenase… · a predicted model of the same protein · chain B 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 P15651
- Elsewhere: RCSB PDB 1JQI · PDBe 1JQI · UniProt P15651
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