MolNFT v1 · #63066 · protein
Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from escherichia COLI
3EY9 · Pyruvate dehydrogenase [cytochrome]: “Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate…”. X-ray diffraction, 4 ligands (TPP, FAD, MG), 10 pockets (best druggability 0.87).…
- PDB
- 3EY9
- Type
- protein
- Length
- 1,142 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase [cytochrome]
- EC
- 1.2.2.2
- UniProt
- P07003
- Ligands
- TPP, FAD, MG, SO4
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) | protein | 571 | 40% helix, 19% strand | P07003 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.87 | 0.88 | 135 | TPP, FAD, MG, SO4 |
| 2 | 1096 | 0.87 | 0.88 | 127 | SO4, TPP, FAD, MG |
| 3 | 95 | 0.47 | 0.81 | 27 | empty |
| 4 | 105 | 0.46 | 0.80 | 22 | empty |
| 5 | 65 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3369 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 3EY9 · Structural basis for membrane binding and catalytic activation of the peripheral membrane… · the same entry in another collection · chain B against B, TM-score 1.00
- P07003 · AlphaFold monomer V2.0 prediction for pyruvate dehydrogenase [ubiquinone] (P07003) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P07003
- Elsewhere: RCSB PDB 3EY9 · PDBe 3EY9 · UniProt P07003
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