Research workbench
Crystal structure of human short-chain acyl CoA dehydrogenase
Analyse Crystal structure of human short-chain acyl CoA dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VIG
- Type
- protein
- Length
- 3,007 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain specific acyl-CoA dehydrogenase,
- EC
- 1.3.99.2
- UniProt
- P16219
- Ligands
- FAD, COS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 379 | 58% helix, 16% strand | P16219 |
| B | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 371 | 58% helix, 16% strand | P16219 |
| C | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 379 | 59% helix, 16% strand | P16219 |
| D | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 375 | 58% helix, 16% strand | P16219 |
| E | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 380 | 58% helix, 16% strand | P16219 |
| F | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 374 | 58% helix, 16% strand | P16219 |
| G | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 375 | 58% helix, 16% strand | P16219 |
| H | Short-chain specific acyl-CoA dehydrogenase, (EC 1.3.99.2) | protein | 374 | 58% helix, 16% strand | P16219 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- COS · Coenzyme A persulfide · ligand · 5 copies · chains A, B, C, D, F, G, H
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, D, E, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.85 | 0.85 | 114 | FAD |
| 2 | 542 | 0.82 | 0.88 | 67 | FAD, COS |
| 3 | 576 | 0.82 | 0.87 | 67 | FAD |
| 4 | 565 | 0.82 | 0.87 | 68 | FAD, COS |
| 5 | 560 | 0.82 | 0.87 | 66 | FAD |
Interfaces
15 interfaces between chains.
- G–H · 1838 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1836 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 1832 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1829 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1618 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2VIG · Crystal structure of human short-chain acyl CoA dehydrogenase · the same entry in another collection · chain H against H, TM-score 1.00
- P16219 · 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 P16219
- Elsewhere: RCSB PDB 2VIG · PDBe 2VIG · UniProt P16219
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