Research workbench
Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase
Analyse Crystal structure of the D444V disease-causing mutant of the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J5Z
- Type
- protein
- Length
- 959 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase, mitochondrial
- EC
- 1.8.1.4
- UniProt
- P09622
- Ligands
- FAD, PO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 477 | 36% helix, 27% strand | P09622 |
| B | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 482 | 34% helix, 27% strand | P09622 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.83 | 0.86 | 75 | empty |
| 2 | 870 | 0.80 | 0.82 | 98 | FAD |
| 3 | 840 | 0.80 | 0.83 | 101 | FAD |
| 4 | 277 | 0.73 | 0.86 | 49 | GOL |
| 5 | 247 | 0.68 | 0.84 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 4010 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5J5Z · Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide… · the same entry in another collection · chain A against A, TM-score 1.00
- P09622 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P09622) · a predicted model of the same protein · chain A 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 P09622
- Elsewhere: RCSB PDB 5J5Z · PDBe 5J5Z · UniProt P09622
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