Research workbench
Structure of the human MCAD:ETF E165BETAA complex
Analyse Structure of the human MCAD:ETF E165BETAA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A1T
- Type
- protein
- Length
- 2,100 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor; Electron transfer…
- EC
- 1.3.99.3
- UniProt
- P11310, P13804, P38117
- Ligands
- FAD, AMP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (EC 1.3.99.3) | protein | 386 | 57% helix, 17% strand | P11310 |
| B, D | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (EC 1.3.99.3) | protein | 387 | 57% helix, 16% strand | P11310 |
| C | Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor (EC 1.3.99.3) | protein | 388 | 56% helix, 17% strand | P11310 |
| R | Electron transfer flavoprotein alpha-subunit, mitochondrial precursor | protein | 313 | 28% helix, 27% strand | P13804 |
| S | Electron transfer flavoprotein beta-subunit | protein | 239 | 28% helix, 31% strand | P38117 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 5 copies · chains A, B, D, C, R
- AMP · Adenosine monophosphate · ligand · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.86 | 0.92 | 73 | FAD |
| 2 | 584 | 0.84 | 0.89 | 70 | FAD |
| 3 | 663 | 0.83 | 0.87 | 71 | FAD |
| 4 | 517 | 0.83 | 0.89 | 65 | FAD |
| 5 | 674 | 0.82 | 0.86 | 85 | FAD |
Interfaces
12 interfaces between chains.
- R–S · 2657 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2434 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 2384 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1791 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1778 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2A1T · Structure of the human MCAD:ETF E165betaA 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
- 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 0.96
- 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 0.71
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 2A1T · PDBe 2A1T · UniProt P11310 · UniProt P13804 · UniProt P38117
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