MolNFT v1 · #96663 · protein
Dihydrolipoyl dehydrogenase of escherichia COLI pyruvate dehydrogenase complex
4JQ9: “Dihydrolipoyl dehydrogenase of escherichia COLI pyruvate dehydrogenase complex”. X-ray diffraction, 3 ligands (FAD, SO4, CL), 20 pockets (best druggability 0.88). MolNFT v1 #96663 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4JQ9
- Type
- protein
- Length
- 2,820 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- C3TQA2
- Ligands
- FAD, SO4, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 471 | 35% helix, 28% strand | C3TQA2 |
| C, D, F | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 469 | 35% helix, 28% strand | C3TQA2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, E, D, F
- SO4 · Sulfate ion · ion · 29 copies · chains A, C, B, D, F, E
- CL · Chloride ion · ion · 11 copies · chains A, C, E, F
- GOL · Glycerol · additive · 10 copies · chains A, B, C, E, D, F
- IMD · Imidazole · additive · 4 copies · chains A, C, E
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 | 1130 | 0.88 | 0.89 | 122 | SO4, FAD |
| 2 | 597 | 0.85 | 0.90 | 83 | SO4, FAD |
| 3 | 998 | 0.82 | 0.83 | 102 | SO4, GOL, FAD |
| 4 | 396 | 0.81 | 0.90 | 68 | SO4, IMD, FAD |
| 5 | 804 | 0.81 | 0.84 | 82 | SO4, IMD, FAD |
Interfaces
5 interfaces between chains.
- A–B · 4088 Ų buried · 43 hydrogen bonds · protein-protein
- C–E · 3969 Ų buried · 42 hydrogen bonds · protein-protein
- D–F · 3965 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 1433 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1151 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4JQ9 · Dihydrolipoyl dehydrogenase of Escherichia coli pyruvate dehydrogenase complex · the same entry in another collection · 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 C3TQA2
- Elsewhere: RCSB PDB 4JQ9 · PDBe 4JQ9 · UniProt C3TQA2
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