Research workbench
Pyruvate oxidase variant E59Q from L. plantarum in complex with phosphate
Analyse Pyruvate oxidase variant E59Q from L. plantarum in complex with phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HAF
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate oxidase
- UniProt
- A0A1A0DLW4
- Ligands
- FAD, TPP, K, MG, PO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate oxidase | protein | 585 | 42% helix, 16% strand | A0A1A0DLW4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.78 | 0.81 | 92 | FAD, GOL |
| 2 | 575 | 0.77 | 0.84 | 62 | FAD, GOL |
| 3 | 86 | 0.66 | 0.91 | 25 | MG, TPP |
| 4 | 105 | 0.66 | 0.90 | 29 | TPP |
| 5 | 256 | 0.56 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1336 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6HAF · Pyruvate oxidase variant E59Q from L. plantarum in complex with phosphate · 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 A0A1A0DLW4
- Elsewhere: RCSB PDB 6HAF · PDBe 6HAF · UniProt A0A1A0DLW4
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