Research workbench
Crystal structure of human dimethylglycine-dehydrogenase
Analyse Crystal structure of human dimethylglycine-dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L46
- Type
- protein
- Length
- 1,617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.09
- Source
- Homo sapiens
- Molecule
- Dimethylglycine dehydrogenase, mitochondrial
- EC
- 1.5.8.4
- UniProt
- Q9UI17
- Ligands
- FAD
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · resolution 3.09 · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethylglycine dehydrogenase, mitochondrial (EC 1.5.8.4) | protein | 809 | 28% helix, 27% strand | Q9UI17 |
| B | Dimethylglycine dehydrogenase, mitochondrial (EC 1.5.8.4) | protein | 808 | 29% helix, 28% strand | Q9UI17 |
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
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.88 | 0.89 | 154 | FAD |
| 2 | 966 | 0.87 | 0.88 | 144 | empty |
| 3 | 646 | 0.87 | 0.91 | 94 | FAD |
| 4 | 235 | 0.79 | 0.93 | 41 | empty |
| 5 | 129 | 0.75 | 0.94 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 5L46 · Crystal structure of human dimethylglycine-dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UI17 · AlphaFold monomer V2.0 prediction for dimethylglycine dehydrogenase, mitochondrial… · a predicted model of the same protein · chain A 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 Q9UI17
- Elsewhere: RCSB PDB 5L46 · PDBe 5L46 · UniProt Q9UI17
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