Research workbench
Crystal structure of human dihydrolipoamide dehydrogenase complexed to NAD+
Analyse Crystal structure of human dihydrolipoamide dehydrogenase complexed to NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZMC
- Type
- protein
- Length
- 3,774 residues
- Chains
- 8
- 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, NAD, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 472 | 35% helix, 27% strand | P09622 |
| B, C, F, H | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 471 | 34% helix, 27% strand | P09622 |
| D | Dihydrolipoyl dehydrogenase, mitochondrial (EC 1.8.1.4) | protein | 474 | 35% helix, 26% strand | P09622 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 36 copies · chains A, B, C, D, E, F, G, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.84 | 0.89 | 66 | empty |
| 2 | 789 | 0.84 | 0.87 | 96 | FAD, NAD |
| 3 | 713 | 0.84 | 0.88 | 75 | empty |
| 4 | 770 | 0.84 | 0.87 | 101 | FAD, NAD |
| 5 | 740 | 0.84 | 0.87 | 78 | empty |
Interfaces
10 interfaces between chains.
- E–F · 4049 Ų buried · 68 hydrogen bonds · protein-protein
- G–H · 4048 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 4032 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3985 Ų buried · 66 hydrogen bonds · protein-protein
- A–F · 668 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1ZMC · Crystal Structure of Human dihydrolipoamide dehydrogenase complexed to NAD+ · the same entry in another collection · chain H against H, TM-score 1.00
- P09622 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase, mitochondrial (P09622) · a predicted model of the same protein · chain E 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 P09622
- Elsewhere: RCSB PDB 1ZMC · PDBe 1ZMC · UniProt P09622
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