MolNFT v1 · #30257 · protein
The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein (didomain) subcomplex of human pyruvate dehydrogenase complex.
1ZY8 · Dihydrolipoyl dehydrogenase, mitochondrial: “The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide dehydrogenase-binding protein…”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.84).…
- PDB
- 1ZY8
- Type
- protein
- Length
- 4,960 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase, mitochondrial; Pyruvate dehydrogenase protein X component…
- EC
- 1.8.1.4
- UniProt
- P09622, O00330
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 474 | 35% helix, 27% strand | P09622 |
| K, L, M, N, O | Pyruvate dehydrogenase protein X component, mitochondrial | protein | 44 | 50% helix, 5% strand | O00330 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.84 | 0.86 | 79 | empty |
| 2 | 656 | 0.84 | 0.88 | 60 | empty |
| 3 | 847 | 0.83 | 0.86 | 69 | empty |
| 4 | 826 | 0.83 | 0.86 | 67 | empty |
| 5 | 869 | 0.83 | 0.85 | 77 | empty |
Interfaces
26 interfaces between chains.
- C–D · 3959 Ų buried · 64 hydrogen bonds · protein-protein
- I–J · 3959 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3938 Ų buried · 61 hydrogen bonds · protein-protein
- G–H · 3861 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 3857 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1ZY8 · The crystal structure of dihydrolipoamide dehydrogenase and dihydrolipoamide… · the same entry in another collection · chain K against K, 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 P09622
- Every structure of UniProt O00330
- Elsewhere: RCSB PDB 1ZY8 · PDBe 1ZY8 · UniProt P09622 · UniProt O00330
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