Research workbench
Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from escherichia COLI
Analyse Structural basis for membrane binding and catalytic activation of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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