Research workbench
Structure of the human MCAD:ETF complex
Analyse Structure of the human MCAD:ETF complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T9G
- Type
- protein
- Length
- 1,960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial; Electron transfer…
- EC
- 1.3.99.3
- UniProt
- P11310, P13804, P38117
- Ligands
- FAD, AMP
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial (EC 1.3.99.3) | protein | 386 | 57% helix, 16% strand | P11310 |
| B, D | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial (EC 1.3.99.3) | protein | 387 | 57% helix, 16% strand | P11310 |
| C | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial (EC 1.3.99.3) | protein | 388 | 56% helix, 16% strand | P11310 |
| R | Electron transfer flavoprotein alpha-subunit, mitochondrial | protein | 184 | 32% helix, 33% strand | P13804 |
| S | Electron transfer flavoprotein beta-subunit | protein | 228 | 28% helix, 30% strand | P38117 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, D, C
- AMP · Adenosine monophosphate · ligand · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.84 | 0.87 | 77 | FAD |
| 2 | 565 | 0.83 | 0.89 | 66 | FAD |
| 3 | 746 | 0.83 | 0.86 | 87 | FAD |
| 4 | 675 | 0.82 | 0.86 | 82 | FAD |
| 5 | 625 | 0.81 | 0.86 | 63 | AMP |
Interfaces
9 interfaces between chains.
- B–C · 2426 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2368 Ų buried · 22 hydrogen bonds · protein-protein
- R–S · 2027 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1800 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1795 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1T9G · Structure of the human MCAD:ETF complex · the same entry in another collection · chain S against S, 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 A against A, TM-score 1.00
- P13804 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit alpha… · a predicted model of the same protein · chain R against A, TM-score 0.99
- P38117 · AlphaFold monomer V2.0 prediction for electron transfer flavoprotein subunit beta (P38117) · a predicted model of the same protein · chain S against A, TM-score 0.99
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
- Every structure of UniProt P13804
- Every structure of UniProt P38117
- Elsewhere: RCSB PDB 1T9G · PDBe 1T9G · UniProt P11310 · UniProt P13804 · UniProt P38117
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