Research workbench
Crystal structures of medium chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate
Analyse Crystal structures of medium chain acyl-CoA dehydrogenase from pig liver… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MDD
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Medium chain acyl-CoA dehydrogenase
- EC
- 1.3.99.3
- UniProt
- P41367
- Ligands
- FAD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Medium chain acyl-CoA dehydrogenase (EC 1.3.99.3) | protein | 385 | 57% helix, 16% strand | P41367 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.81 | 0.86 | 68 | FAD |
| 2 | 576 | 0.81 | 0.87 | 64 | FAD |
| 3 | 61 | 0.73 | 0.98 | 20 | empty |
| 4 | 52 | 0.70 | 0.98 | 16 | empty |
| 5 | 248 | 0.53 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1771 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3MDD · Crystal structures of medium chain acyl-CoA dehydrogenase from pig liver mitochondria… · the same entry in another collection · chain A against A, TM-score 1.00
- P41367 · AlphaFold monomer V2.0 prediction for medium-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 P41367
- Elsewhere: RCSB PDB 3MDD · PDBe 3MDD · UniProt P41367
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