MolNFT v1 · #5384 · protein
Structure of T255E, E376G mutant of human medium chain acyl-CoA dehydrogenase complexed with octanoyl-CoA
1EGC: “Structure of T255E, E376G mutant of human medium chain acyl-CoA dehydrogenase complexed with octanoyl-CoA”. X-ray diffraction, 2 ligands (CO8, FAD), 13 pockets (best druggability 0.84). MolNFT v1 #5384 on GenesisL1: 3D structure…
- PDB
- 1EGC
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Medium chain acyl-CoA dehydrogenase
- EC
- 1.3.99.3
- UniProt
- P11310
- Ligands
- CO8, FAD
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Medium chain acyl-CoA dehydrogenase (EC 1.3.99.3) | protein | 387 | 56% helix, 15% strand | P11310 |
Ligands and binding sites
- CO8 · Octanoyl-coenzyme A · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.84 | 0.88 | 78 | CO8, FAD |
| 2 | 1001 | 0.84 | 0.85 | 119 | CO8, FAD |
| 3 | 826 | 0.83 | 0.85 | 90 | CO8, FAD |
| 4 | 746 | 0.83 | 0.86 | 81 | CO8, FAD |
| 5 | 1146 | 0.79 | 0.81 | 91 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2479 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2394 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1755 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1737 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1EGC · Structure of T255E, E376G mutant of human medium chain acyl-CoA dehydrogenase complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- P11310 · AlphaFold monomer V2.0 prediction for medium-chain specific acyl-CoA dehydrogenase… · a predicted model of the same protein · chain C 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 P11310
- Elsewhere: RCSB PDB 1EGC · PDBe 1EGC · UniProt P11310
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